Stargate: The Ascension of the Fifth Race
by Jayan phoenix
Summary: This story will follow the events of Stargate Atlantis and show how the people of Earth take on their new role given to them by the Asgard. Sheppard Steals the city of Atlantis and returned to Pegasus to create a new Lantean society which he hopes to be able to fight the Wraith but in the Milky Way things are changing, and will not remain the same.
1. Chapter 1

**Chapter One**

**Atlantis Returns to Earth**

The Sol system within the Milky Way Galaxy was birthplace of humanity thousands of years ago, whilst humans had been displaced by various alien races over the years, the Humans of Earth had developed without falling prey to perils of the Milky Way.

The humans of this small isolated civilisation was legendary across the Milky Way Galaxy, only twelve years previously had they began exploring the Galaxy using the Stargate Network, in that time they had risen high.

They had been to war with the Goa'uld, a race of parasitic alien lifeforms, they had fought hard and achieved great victories, then they fought the Replicator menace, a race of technological lifeforms that had nearly destroyed one of the most technologically advanced races known to the Galaxy, and finally they had destroyed the race of ascended beings known as the Ori from a distant galaxy.

Whilst all of this had been ongoing, only a small number of the inhabitants of the planets were aware of the planets role in the Galactic affairs, and it was only three hours since a new enemy had been engaged over the planet.

The Wraith were a race of humanoid creatures that were native to the Pegasus Galaxy, they fed on human life with a feeding organ on their hand, their native Galaxy did not have the food source they required so they had travelled to Earth using a Hive ship, their largest ship and had attacked.

The hive ship had utilised a powerful new source of power, a ZPM, and with it they had been able to defeat Earths defensive fleet, but just in time and using an experimental new propulsion drive that created a wormhole, the city-ship known as Atlantis returned to Earth for the first time in thousands of years and defended the planet whilst the ship was destroyed from within.

The City had landed in a private bay off the coast of San Francisco, it was privately owned by a American billionaire but the US government and its allies had rented it for the time being, the city was sheltered within the bay, and US ships were guarding the entrance to prevent the great city being discovered.

The city was covered in a cloak to prevent the general public from discovering it, the ZPM's that powered the city were greatly taxed by powering the cloak constantly, but the city had received seven Mark III naquadah Generators to compensate.

Standing in Stargate operations within the city was Richard Woolsey, the former leader of the expedition of Atlantis, no longer was he in charge of the expedition but he was in charge of the city until relieved.

The City had not been dormant since it returned, the moment they had touched down on the water, automated systems had initiated. The sensors swept the planet and the city went into a temporary slumber whilst it settled itself.

"Doctor McKay, please can you come to Operations?" Woolsey said into his ear peace after the technicians were unable to reboot the systems.

"On my way." Rodney replied over the radio, "I have just finished calibrating the generators; they should last for a few weeks at least."

He only took a number of minutes before he arrived from the transport booth.

"Still offline?"

"Yes, all stations are offline, and the systems will not respond" Chuck told him

"Right well let me take a look" Rodney said and he pulled a laptop towards him, "I think the city is scanning the planet, but I have no idea why –"

The city systems suddenly began to reboot and all displays woke again showing them telemetry for the planet. The city had locked onto the Terra Atlanus, the Antarctic Outpost for the Ancient Weapons platform, but the city also detected the SGC operating out of Cheyanne Mountain, and Area 51 in Nevada.

They city's own long range sensors were also delving into the deep space of the Milky Way, however the City's systems were not the only thing that caught the eye of the City's people, the Stargate that sat down the steps in front of the stain glass window suddenly shut down, and from the floor a set of automated claws rose up and gripped the gate.

"Doctor McKay?" Woolsey asked startled.

"I don't understand"Rodney said stepping forward,

The gate was lifted out of the floor, but the floor also then raised itself. The gate was swapped with a Milky Way style gate, whilst the gates on this network looked nearly identical, the new gate was golden in colour with the red chevrons.

The gate was raised to the same position previously occupied by the Pegasus gate.

"I never knew that was there!" Rodney said walking down the steps to look at the gate, "I carried out a detailed scan of this floor after the lockout device used by the Lanteans, but I did not get any readings on this."

"Rodney this gate is old" Zelenka said looking at it, "but it has the same point of origin symbol as Earth."

"That's impossible" Rodney exclaimed "our symbol came from the gate Ra brought to Earth, that would mean that the Goa'uld somehow changed the symbol, but why?"

"Well the symbol does resemble a pyramid and a sun, and he was the god of the sun." Woolsey said, "Why wouldn't he keep it."

"No –"Rodney said staring at the gate carefully, "the symbol is slightly different, the circle has marks on it, It's a Stargate!"

"Well it stands to reason; the network was built from Earth." Zelenka said shrugging, "the Ancients must have taken the Earth gate with them in case they ever returned but placed a second gate within the outpost for the planet."

"maybe, but why has the city changed gates? The Pegasus gate would take precedence automatically." Rodney said and he stormed back up to operations and checked the systems.

"Atlantis this is General Landry at the SGC" came a voice over the radios.

"Go ahead General" Woolsey replied

"I don't suppose you will know why our gate systems just turned off" he asked

"I think we might have an idea" Woolsey said raising his eyebrows in surprise.

"General" McKay said tapping into the frequency, "Atlantis has changed the gate that sits in our gate Room to a Milky Way gate, however this gate is the original to this planet and I would guess that the city and gate network has deactivated yours for that reason."

"Can you not deactivate your gate?" he asked

"No, the system was automatic and I have found no access to it." Rodney said.

"Doctor I have seven off world teams scheduled for check in within the next two hours and a further seven teams waiting to go off world. We need our gate back up and running." General Landry demanded.

"General, I think for the time being Atlantis can deal with all off world travel" Woolsey said "At least for the time being before a permanent solution can arranged"

"Very well, for now please have your Atlantis Reconnaissance Teams stand in for now, I will have the SG teams transported over. Landry out."

Over the next number of weeks Atlantis has seen a great many people walk its corridors, Stargate Command had temporarily been relocated to the city, the SG teams and AR teams had merged to become a united team of people traveling the Milky Way.

John Sheppard for his services whilst Ranking Military Officer was given the promotion to Colonel, whilst Evan Lorne was promoted to Lieutenant colonel, other personnel were similarly advanced.

The Atlantis Science teams were kept on the city permanently, as had the operations technicians, Sheppard had gone direct to General O'Neill and asked for this to prevent accidents on the city, the great technological wealth on the city was to be researched and catalogued but a great many areas were locked down to prevent over eager scientists from tampering with technology they didn't understand.

Whilst the Battle of the Super-Hive had been going on, the Odyssey has been unavailable due to a secret mission, it had been sent to a distant planet to set up a new base to study the planet core and to research the mystery of the ninth chevron, the area was a hot spot for the Alliance and was unable to return.

Now standing guard over the Planet was the USS Daedalus, Apollo, Odyssey and the newly completed George Hammond, on the planet the Sun Tzu had been brought home from its battle with the Super hive via the Odyssey's tractor beam technology.

The BC:304 had seen significant upgrades since the Daedalus had been built, with the Asgard upgrades strapped onto the Odyssey, and advances in Earth design and data from Atlantis, the new Mark II ship was built from the ground up with all of this technology.

The Hammond was the first Mark II built and its systems were the most advanced, better shielding, weapons and power generation. The Captain of this ship had been debated but it had been given to Brigadier General Samantha Carter, a legend to Earths Stargate Program, former member of the SG:1, Former leader of the Atlantis Expedition, a women who had pushed Earth technology into a new age and had been instrumental in the defeat of the Goa'uld, Replicators, and the Ori, but also the Lucian Alliance and the Wraith battles.

The Odyssey still contained the Asgard Legacy and it was being studied continuously, Daniel Jackson had been assigned to the ship to help with the translation and learning, but the commander of the ship was also a former member of SG:1 was Brigadier General Cameron Mitchell, having proved his ability as a ship commander in the expedition the Celstus Galaxy where they had discovered the Ark of Truth and finally ended the Ori, the ships command was given to him permanently after he returned from the To'kra homeworld.

Further ships were planned to be built, the BC:304 was a proven design and its production would continue, the BC:303 Prometheus class vessel was also to be built again although it would be known as the BC:303b, unlike the original Prometheus, the ship was built much like the BC:304's with all the technology built straight in from the beginning. The ship was to be used as a scout and science vessel, but it was still a capable ship for space battles, and it planned to act as a support ship for any future expeditions to free up the larger Class of vessels.

The Atlantis database had been studied greatly by the scientist, they had attempted to create a direct copy of the database but the security had prevented it, so they were forced to study selected portions on the cities terminals.

They had found a nine chevron address within the Database which was been studied by the Icarus Project, but there was a more pressing concern, the future of the city.

Nobody could agree with what should happen with the great city, some wanted it to return to Pegasus, others wanted it in the Milky Way to become a the first off world colony, others wanted it left on Earth to be the SGC and Homeworld Command as an international facility.

However a large faction of the oversight committees wanted the city to be stripped of all salvageable technology and material and scrapped, as they did not see what function it had. They believed that the Pegasus Galaxy was too far away to care about and they were not a threat to Earth so leave the Wraith to their corner of the Galaxy.

Richard Woolsey had not agreed with his fellow members of the IOA, and he along with O'Neill, Carter and Sheppard were all pushing for the city to return to Pegasus, they had woke the Wraith, they had an obligation to prevent Human life from being destroyed, but also they would have no warning if the Wraith found a way to Earth.

/*****************************\

So this is a re-post of my original story, This will be much more detailed than the original and will fill the gaps between the three series and I hope to go further.


	2. Chapter 2

**Chapter Two **

**Destiny of Atlantis**

A month and a half after Atlantis arrived on Earth a decision had not been made for the future of the city, none could agree of what to do but Colonel Sheppard had petitioned for Teyla and Ronon, both native to the Pegasus and they had been trapped on Earth because they had wanted to help them fight of the Wraith and they should be able to return home.

The IOA had argued for a week on the issue and they had decided that they couldn't spare a ship to take them back nor would they utilise a ZPM to dial another galaxy. John had gone to Carter and asked for her help and she had understood their plight, with her ship recently finished its rundown across the Milky Way.

She had gone to Jack's apartment in Washington using beaming technology to prevent the IOA from finding out about their conversation, Jack had agreed and as commander of Homeworld Command he had jurisdiction over all of Earths vessels, although his authority over the Sun Tzu was tenuous.

He greenlit the mission, the Hammond would travel to Pegasus and return Teyla and Ronon to the new Athosian settlement, she had beamed directly back to her ship and began preparations, the ship left the next day, the excuse Jack had used to appease the IOA was that the Hammond needed its engines tested on a long voyage and this killed two birds with one stone.

Teyla was returned to her people and the Hammond did some recon and the discovered that the Wraith were consolidating again but there were two factions forming, but the smaller faction was possible lead on Todd's allies.

Ronon had decided to stay with John on Earth, he had joined with the SG teams a number of time to relieve the tedium of Earth, he also took Teal'c up on his offer to visit him and the Free Jaffa Nation. Ronon was welcomed by hostility by the Jaffa on Dakara where they were rebuilding their nation's capital after it had been destroyed by the Ori.

John was not worried about Ronon, Teal'c had guaranteed him that he would be returned alive, but the trials of combat would be long and Ronon had told John under no circumstances was he returning until he had beaten all of Jaffa who challenged him.

John was not happy with any of the SG teams that he was assigned to, he was given the choice of which ever personnel that he wanted but he had not been able to find a team that he worked well with, but the truth of the matter was that he couldn't stop thinking of Pegasus.

With Atlantis becoming the stand in for the SGC, John had taken command of the city as its leader, General Landry was overseeing the upgrades being carried out to the SGC facility, and he was also going to be taking some down time for the first time since he took over from Jack.

Woolsey had been sent to Washington to support Jack in his debates about Atlantis, but John didn't really mind as it gave him free reign over his city. The IOA had refused to allow the city to be repaired, as they still wanted the city destroyed, but he was secretly having the Atlantis engineers repair the city, the lower levels that had been flooded when they had first arrived on the city and when the storm had hit the city whilst the Geni had seiged them: the Replicators had repaired some of the city but further repairs were being carried out.

A number of the city's towers were being repaired after the damage caused by the asteroids when the left Lantea for New Leantea, the repairs were being carried out carefully, John had had a second cloaking device added to the city whilst the work was carried out, the IOA was sniffing around and he knew that they wouldn't agree.

John was not an poor man, his father had a great deal of wealth and had been a powerful American businessmen, his brother had taken most of the wealth and had taken over as CEO of the company but John has access to funds if he chose and he was using all the pull he could buy and persuade to have the city return to Pegasus.

Dressed in his military uniform he travelled to Washington to meet with the IOA and O'Neill for the final decision on the city.

"I am not going to lie to you Sheppard, I do not know how this meeting will go" Jack said as they travelled to the meeting location, "The IOA can never be predicted, but we have allies in the British, but they are not being very cooperative at the moment, their ship is being built at the moment so we might be able to count on them."

"You know that Rodney found a new weapon on the city don't you sir?" John said glumly, it had been quite a shock when McKay had accidently triggered a weapons system they had not known about, three large weapons platforms had deployed on the three piers that did not have drone silos, and if Rodney was correct these were powerful weapons, the Ancient Defence satellites were a similar technology but these were powered by the ZPM but with the weapon now known the information was located within the database.

"Yes, very bad timing but you can't turn your nose up, if it comes to a fight they might be useful, although it would have been better if he could have stopped his tampering with the city for a week, the IOA will not want this technology to slip away, especially with the fight with the IOA heating up."

"Well Rodney is never known for his moments," John smirked "but I am telling you now that city will be returning to Pegasus, even if I have to steal it and take it there myself."

"Careful Sheppard, that is dangerous talk and if I was any other general you could possibly be court martialled." Jack warned "We will see how this meeting goes before we plan further."

They remainder of the journey had gone by silently, Sheppard was not in the mood for talk, he was planning his speech to the committee and it was now more than ever that he wished that an old friend was here, she would have known what to do and say, but would have had more favours that he did to pull strings.

She was a women that he had great respect for and he missed her, if things could have been different he would have sacrificed himself to save her at least with her alive their city would not be in danger.

When they arrived they went made to wait an hour after their supposed start date, which only fuelled Johns annoyance more, but eventually they were sat down in front of the higher members.

"Colonel Sheppard and General O'Neill, thank you for waiting, we needed further time to discuss the issue you brought before us." Carl Storm said looking at them "The issue of the City of Atlantis has been discussed thoroughly and we have finally come to a decision."

"However before our decision has been made, we would invite you to have your final input into the debate" Mr Chapman the British representative said.

John stood carefully and regarded them coolly "As you know the Alterans escaped this Galaxy in Atlantis to out run a plague, once there they built their new empire, the city of Atlantis was used as their base and the seeded life in that Galaxy."

"The city is a symbol of hope to that Galaxy and in our short amount of years there we were able to win many battles against the Wraith, a feat only accomplished by the Alterans before us. I know that you want to strip the city down for its technology, but Pegasus was the site of an empire, there are many planets that have Alteran outposts and technology, we discovered warships and power sources and other technologies, If the Wraith were to gain this technology to travel to the Milky Way you would be allowing them to pray on the humans of this Galaxy, just as you would by opening the door yourself."

"I would remind you Mr Storm" Jack said "that the president has pledged his support for the Expedition to continue, he does not feel that the City should be destroyed. Your own representative Richard Woolsey has also stated on the record that the City should return. As commander of Homeworld Command I would much rather have the city in Pegasus to be a defence of Earth, without it the Wraith will seek to come defeat them before coming to Earth."

"Yes, Yes General we have heard your views before, however the Atlantis Expedition was an international operation, and therefore your government is only one voice of many that needed to be convince." Storm stated, "And our backing is being placed on the Icarus project."

"The Wraith are not an immediate threat to this Galaxy, the Alliance is stepping up its war against us and there is a small coalition of Goa'uld that have gained a foothold over three planets, and the Free Jaffa are still rather hostile towards us." Shen Xiaoyi said "the technology on Atlantis alone is enough for us, with the new weapons systems we will be able to reverse engineer our own version and we will have the technology we need to defend ourselves."

"That is a mistake!" John exclaimed "There is more in Pegasus than we already have! You are allowing the death of thousands to save yourselves!"

"Colonel, would you rather save the lives of humans in another Galaxy over those of your own planet" Shen Xiaoyi said " We have the Asgard and Ancient database here on earth what more do we need, we have the technology to defeat any threat, but we can trade to prevent hostility."

"You cannot be serious!" Jack shouted "You cannot trade any technology from Atlantis or from the Asgard Legacy, That is above your purview."

"No the technology on Atlantis falls under our jurisdiction General." Storm stated firmly.

"And what is your decision for the City?" John asked losing his patience.

"All salvageable technology is to be removed and sent to Area 51 for further study, other systems will be removed and placed within a New IOA facility. The database will also be transferred but the remaining structures will be dismantled and useable materials will be recycled." Shen Xiaoyi stated clearly.

"And when will this happen?" Jack asked distaste showing on his face.

"Within the next six months" Jean LaPierre the French representative told him, "The city will remain as the acting SGC for that time whilst Cheyanne Mountain has its upgrade. The chair will be used of Earth defence so all of the ZPM's will remain for now."

John went to stand and opened his mouth to argue but Jack placed a hand on his arm to stop him.

"Then as Commander of Homeworld Command I would have the city turned over to me for the next six months as it is the acting SGC and the only defence Earth has." Jack demanded, "After the six months is over you can do what you want."

The IOA representatives did not speak for a moment as they looked at him speculatively.

"I find this agreeable" Mr Chapman stated looking around "Atlantis is a home to the expedition but General O'Neill is correct, it falls under his jurisdiction as Commander of Homeworld Command, I would also point out that withholding it would be against the agreement that we ourselves signed."

"Agreements can be Changed!" she exclaimed "This is unacceptable."

"No" Jean added "this is following the procedure that the IOA has set for the planet, and it will take 6 months of the agreement to be changed anyway."

The French and British representatives were receiving cold looks from the Russian, American and Chinese members but it seemed that they had no choice but to agree the decision, but they were not happy.

Jack had been forced to nearly strong arm Sheppard out of the room and into the car.

"What was that Sir!" he shouted

"That was me buying time" Jack said "you were lucky your friends in France and Britain were able to find a way around the others."

"They did nothing!" John exclaimed angrily "They gave us six months."

"Yes, but that was all they could get you as they have to operate within the confines of their own authority, and by pointing out to us that they had six months it prevented the other nations from premature destruction." Jack explained "I was able to get them to agree to doing just that, your own efforts got them onside, but they could not find a way to help, I just gave them a way."

"But what good is six months?" John asked

"Much can happen in six months Sheppard, You should know that." Jack told him, "however you should now feel good that we do have some friends."

"And you are now in command of my city." John commented, "What do you plan for the city General?"

Jack shrugged "Well I think it would be a good idea to see what supplies the city would need for a full expedition. In case we ever built a city-ship in the future it would be good to know. I would also like to see a report on the full diagnostics of the shield and star drive."

John paused and nodded frowning, he wondered if he was getting a hidden message from the General, but even if he wasn't, he had a plan in his own mind, and people to get to the city. Doctor Weirs dream was still far off, but he hoped he was striding towards it.

/*****************************\

So the IOA is still up to their tricks but Jack is no slouch.


	3. Chapter 3

**Chapter Three**

**Return to Pegasus **

It had been two weeks since John and Jack had been in the meeting with the IOA and it had been a very busy two weeks for the both of them, John has reached out to all members of the previous expedition and made enquiries to see if they would be willing to return to Pegasus, but told them that it was possible that they would be out of communication with Earth for some time.

The response had been very positive and nearly every member of the expedition signed back on for another tour. It was still the common consensus that the people of Earth owed aid to the Pegasus galaxy but they also believed that there would be further gains to be made if they continued to explore the second home of the Altera.

Jack had also added people to the expedition roster, adding another hundred people with various skills that they would need. Atlantis personnel had previously mostly consisted of scientists, medical staff, soldiers, and support staff. Jack had assigned them archaeologists, linguists, but most importantly mechanical engineers and structural engineers, this city could need repairs and they would need the people to do it.

Once all who had agreed had been briefed in secret their belongings had been sent to the city, and slowly the people were also brought to the city but in low numbers to avoid suspicion. The cities immense size meant that they were able to use parts of the city that had previously been left unused to prevent discovery. John had been able to purchase the supplies and resource stocks himself using the money that he had inherited from his father, and he had asked his brother for more, whilst John couldn't tell him the reason why he told him a vague answer which his brother bought after speaking to Johns ex-wife.

Weapons had not been an easy purchase to make but Jack had pointed him in the direction of an old acquaintance who dabbled in the black market, and he had been able to acquire the weapons that they needed, but also the equipment and supplies to make further ammunition should they require it.

Current technology research and development, including some prototypes were also transferred to Atlantis from Area 5, with the pretence of further research by the Atlantis staff using the Atlantis Database. But the Technology was sent straight to the storage rooms for later use. Eventually after four weeks of planning and work the city was ready to leave Earth for a second time in its known history. Jack had yet to green light any change to the city's location, he was playing this very careful, he had visited Britain and France to seek the approval of their highest level of government to sign a document that would back his order over the IOA's intervention, it would not mean much but it would allow him to save his job and stay in command of the planets defence.

The Russians has also agreed to the proposal, Jack had gone with Daniel to negotiate and they had agreed as they did not like the IOA. With four of the five gate Alliance signatories in agreement, he was happy for the plan to go forward. The last part in his plan was the acquisition of three near full ZPM's from Earths stock that had perhaps been one of the trickiest items for Jack to get, but with the salvage from the super hive they had a number of them which had been swapped for Atlantis' own used ones.

It had taken a further six weeks before the city was truly ready, Doctor Rodney McKay had told John that the city could not leave and fly them back to Pegasus until every system had been checked and diagnostics run to ensure that they were functioning, he was still annoyed about the use of the wormhole drive and the damage it did to the city systems.

If they were to fly the city away it was very likely that a fault could cause them to drop out of hyperspace or even perish in subspace. So Rodney and his team which included the large number of engineers spanned the city checking every system for problems, but only found minor deterioration in places which they quickly repaired.

They had integrated the MarkIII Naquadah generators directly into the power distribution system, they could not power the stardrive but they would add additional power to the city whilst in transit to reduce the drain on the ZPM's, it was hoped that they would save another power to be able to fly the city again if needed but also to have power to defend the city with the shield and weapons if needed.

McKay had been pulled away from the city unexpectedly which had caused a further delay, he had designed and drawn up the plans for a Subspace Capacitor, which was hoped to be the next power source for all of Earths vessels. They were a compromise, they offered infinite amounts of energy unlike a ZPM, but the draw back was that they could not channel the same amount of energy at one time and only offered a seventh of the power of a ZPM that was at full capacity. The prototype had malfunctioned so Rondey was requested to assist in fixing the problem as he was its co designer along with Samantha Carter who was unavailable as she had been sent to distant planet on her ship.

Eventually the city was finally ready and waiting for the go from Jack, and he decided that it was time for them to leave, he flew from the Pentagon to Atlantis in a borrowed Puddle Jumper deciding how he would deal with the final issue on problem was the IOA representative who had formally been appointed its leader, Richard Woolsey. Whilst time as the Expedition Leader had changed him, he still held high respect for the IOA and Jack wasn't sure he could trust him, especially since he had been back he had hardly been seen as he underwent an exhaustive debrief with the high IOA members.

The IOA had recently reassigned him back to the City to oversee the Stargate Operations and also to keep an eye on John as they felt he could try to gate back to Pegasus, and Jack had smiled to himself at that tid bit of information, they had reason to suspect John but they had not been far off the mark of what was planned.

Jack arrived in Operations he found Woolsey there speaking with the system technicians with his back to him, covertly he pulled out a 'Zat that was concealed in his pocket and stalked towards the man.

"Why are you all in Operations? there are no off world teams and nobody is going off world for the next few days whilst all teams undergo a full evaluation," Woolsey asked Chuck "Five protected planets have been attacked, and we believe that there is someone communicating with the Lucian Alliance, have you found any subspace broadcasts or cloaked vessels as I asked you to search for them?"

"No Mr Woolsey, the City sensors have not been able to detect any cloaked vessels entering the atmosphere or in orbit, however the sensors have been turned off for technicians from Area 51 to study a number of times, so they could have entered the atmosphere during that time, the IOA demanded that we comply."

Jack frowned, he had not known about that, and it made him feel uneasy especially when key members of the IOA were pushing for the protected planets treaty to be scrapped, and to leave most of the planets to fend for themselves, a decision he opposed greatly, Thor had entrusted them with a responsibility and he would not let the Asgard down.

Jack did not waste another moment and shot Woolsey with the energy based weapon and he slumped immediately to the floor.

"General?" John said waking towards him

"It's time" Jack said smiling "Remember radio silence for the foreseeable future, and when communication is to be established wait for my signal. I will take Woolsey back with me."

"No, sir leave him here. We could have use for him." John requested looking at the man deep in thought.

"If you are sure, just don't kill him, this city is now in your care Colonel Sheppard, if you do your job correctly you will remain so when the IOA pulls their heads out their -"

"Asking for one more thing Sir, We will need a ship." John said quietly.

"The Daedalus will be with you in Pegasus, Officially it will be sent to retrieve you all, however once in Pegasus you will need to remove the locator beacon." Jack said vaguely "I would also have the city searched just in case, it wouldn't be a surprise if subspace transmitters were installed."

"Yes Sir" John said standing to attention and saluting "You should go now sir."

"Good luck." Jack said and he left quickly.

John walked over the nearest console and pressed a button to open a city wide broadcast

"Attention all personnel,We will be returning to the Pegasus Galaxy. The Wraith are still a plague on the human population and our off world allies have been alone for nearly a year. But it is time to go home, so if you could all make your way to your designated areas we will be back in no time at all."

There was a round of applause from the people in the control room

John finished the announcement and turned to Amelia, "Has General O'Neill's Jumper left the city?"

"Yes sir, he is well on his way." She replied checking her screen.

"Well I think it's time to fly." John said and he quickly left them but called loudly"Put Woolsey somewhere out of the way and lock the door!"

The Chair Room was empty when he arrived, the moment he sat in the chair it activated glowing bright blue and reclining, John could feel the power of the entire city ship coursing under his fingertips and he could sense every person within it and all its systems were available to him.

With the city just outside the city of San Francisco he had to be very careful to avoid the detection. Powering the stardrive and inertial dampeners, the ZPM was utilised for this whilst the other generators were currently powering the cloak to prevent it being discovered, the noise would be very loud but he knew that USAF would come up with some excuse. The ships powerful engines raised the great city out of the ocean slowly and he increased the power gradually and began bring them higher into the sky.

He became aware of alarms in his mind, it was warning him that he needed to activate the shield as the city structural integrity would be severely compromised if they went further, not to mention he war aware of the rise of temperature on the towers and piers.

The moment he was over the cloud bank he transferred from cloak to the shield which drew on more power and activated the full power of the stardrive and city punched out of the atmosphere with a grace that could not be matched by any vessel in the known universe.

Once the city was out in space, John received automatic telemetry and proximity alerts on the observation display, there were five ships in orbit around the Earth, the _Daedalus, Apollo, Odyssey, George Hammond, Sun Tzu_ they powered up their sublight drives and accelerated towards the city.

"This is Colonel Ellis of the _Apollo_, Atlantis why have you left Earth? We have received orders to advise you to return to the Planet," Came a voice over a short range broadcast that was shielded from the other ships.

John ignored them and tuned out the communications that were being sent at the city, he had to admire the lengths that the IOA were going to as the _Hammond_ opened fire with its plasma beams, John knew that Sam was commander of that ship, but the sensor readings told him that she was not using full power, and had targets areas of the shield which covered empty space.

He then diverted all power to the stardrive, and using more power a hyperspace window ripped open in front of them and they plunged directly into it traveling at speeds that even the Odyssey with its Asgard Core and ZPM would not be able to match.

Whilst flying in hyperspace the city required a constant presence in the chair, and the position was mentally taxing and would require a change over after a number of hours, but the only possible replacement was Doctor Becket who had the necessary apptitude and concentration for flying the city. Rondey had told him that even the Altera would require a change in pilot.

The city was alive in his mind, he received a direct feed of the ships data and condition, he could sense the power being drawn from the power devices, feel that power being transferred through the power conduits. The strain on the shield was high but he was not worried about it, his concern rested with the inertial dampeners on one of the piers as he could feel a fault in one of them and he sent a team to begin repairs.

They had managed to travel the great length of the Milky Way in less than a day, they were an hour away from the galactic void where the Midway station had once sat. John was fatigued and needed to swap with Carson, whilst sitting in the chair the body fell into a form of slumber, which Rondey had explained was to reduce the number of rotations of crew. He was about to call for Carson to relieve him when he noticed that Rodney was coming towards him in great haste.

It surprised him as all of the scientists were using the trip to study the technology in greater detail as they had never used it to fly such a great distance and Rodney was monitoring the system to make sure they did not damage a system of expand too much power.

John opened the door to allow Rodney enter.

"Sheppard!" Rodney called racing into the room "I just realised something."

"What Rodney" John said annoyed, hoping that he could leave the chair soon.

"The Tria!" He replied with a look of a child at Christmas.

"What about it" John asked confused thinking back on the Alterans who had been found on the ship.

"At this very moment it is sitting in the void between the two galaxies, an Ancient warship that is not of use to anyone." McKay said excitedly "we should drop out land the Tria on a pier and then continue to Pegasus, we could study the ship and hopefully be able to reverse engineer the ships technology, imagine the advances that we will make with an actual ship to study."

John didn't say a word, but as his thoughts focused on the ship, Atlantis brought up the ships last known location and calculated that it was only an hour away. Atlantis could use a second ship in the coming months, "Well I do not see a problem with that."

The City dropped out of Hyperspace for a moment before opening another window and going back into Hyperspace to reach the ship.

An Hour and Thirty minutes later, the Tria had been was safely docked on the east pier after a landing system had initialised, the ship had passed directly through the shield much like the Pegasus Asgard had once done. The ship had initialised a program that plotted its descent onto a pier, the programed was recognised by the city and docking clamps rose up out of the pier and attached themselves to the ship.

John had sealed off all access to the pier and returned the city to hyperspace towards their destination. Once they were underway he righted himself in the chair and summoned Becket to the chair room and they swapped places.

For the last leg of the journey Becket flew the city to the system that Atlantis would call home, the journey had taken them just under two days if the unscheduled stop off for the Tria from the time scale, the city hyperdrive was the fastest drive known to Earth.

Once inside the new system the city began to de-accelerate and a planet was growing closer, the planet was composed of a vast ocean and they would need to land shortly. Becket left his post and relinquished to the now rested John Sheppard.

John piloted Atlantis into a geosynchronous orbit over that now dwarfed the city-ship, once they had settled into orbit he began the next stage of the landing, re-entry of the planet. Flying a city was a lot harder than flying a F302 and he was forced to concentrate hard.

"Sheppard!" Rodney called over the intercom "You need to slow us down, we are coming in way to steep and it is burning up power that we will need later."

John had to bite back a sharp remark but sent an extra burst of power to the drives and slowed their decent and the friction on the shield was reduced and they were burning less power. The city levelled out and the great fireball that had been created by the friction dissipated and it flew over the oceans below. The stardrive was still powered up and John began to decrease the power and the city lowered itself into the water.

The landing was far superior to their previous ones and John was rather proud of it. Once the city had settled on the ocean surface he deactivated the shield and activated the sensors of the city. The city began to deactivate the flight systems and the power levels entered acceptable levels. The lockdowns that he had implemented was also removed and the people on the city could freely move.

When he was certain that his job was finished he sat up in the chair and the blue light died.

"Rodney, how much power did we use?" he asked walking out of the chair room and tapping into the radio.

"Power was drained from all three ZPM's, but we only used four tenths of the maximum power" Rodney explained happily. "The generators we installed have reduced our power requirements but I would guess that they will have been heavily drained."

"Good" John said and he walked into the Stargate operations where most of the expedition personnel were standing"I want fifteen Atlantis Reconnaissance teams sent out, make contact with our off world allies and trading partners, I want to know what has happened since we left."

"What about Earth?" asked Major Lorne

"We do not communicate with them until we know it is safe, O'Neill will tell us when that is." He explained firmly not wanting any argument "for now we are independent."

"Like we were in our first year with Weir in charge" Chuck said sadly

"But we are better prepared" John said encouragingly #"lets hope we do not wake anything else this time round. Now Ronon you should go find Teyla, she should be on New Athos, Becket can fly you there in a 'Jumper"

They left the room quickly and John turned around to look at everyone, he walked over and pressed a button opening a city wide channel,

"As of today we are on our own, I will not lie to you our departure was not entirely authorised and there will be repercussions, But it is my hope that we can push the wraith back and reduce their numbers to the point of defeat like we have done for the Goa'uld and the Ori and even the replicators. Doctor Weir brought us here with the hope that we would meet the Ancients, and discover the wonders of Atlantis"

"We met an ascended Lantean Alteran, we discovered the city, but as the children of the Altera it is time for us to ascend from the simple humans of Earth to the Lanteans of Atlantis. This is our home and we will protect it! We will succeed where the first Lanteans failed. We are back on Lantea, the planet where it all began and we shall not stop until the Wraith are no more."

A round of applause sounded across the city and the people agreed with their leader, but it was short lived as Richard Woolsey came walking into Stargate Operation and looked angry.

"The IOA never agreed to this" he said

"Mr Woolsey" John said with delight "I see you have got straight to the point."

"Who gave the order to return Atlantis to Pegasus, it was agreed by the IOA that the city would not return, but it would not be decommissioned." Woolsey exclaimed and he pointed at a technician "dial the SGC now!"

"Ignore that order" John commanded "Woolsey you are no longer in command of this city, I am, you are only here as a negotiator and diplomat, you are here at my discretion and so as to not alienate the IOA if and when we re-establish links to Earth, then you can report everything I have done."

"You cannot do this" Woolsey shouted

"I think you will find I already did." John said "now I have to re-establish contact our friends and I am sure we will need your help, you can either help and or you will be restrained to your quarters indefinitely."

Woolsey stood standing for a long moment but seemed to steel himself but did not move.

"Good," John said grimly "I am sending you as an envoy to the Coalition of Planets we should announce ourselves to them."

"Very well." Woolsey said "when do I leave?"

"The moment you have changed into Atlantis personnel uniform" he said, and he walked away laughing at Woolsey's face as he looked down at his suit.

/*****************************\

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	4. Chapter 4

**Chapter Four**

**Formation of a new Lantean Society**

It had been three hours since the City had touched down on the oceans of Lantea, the Expedition members were busy getting back into the swing of the Pegasus Galaxy. The teams that John has sent off world had brought back disturbing news, the Wraith that the _George Hammond_ had detected when it had returned Teyla to New Athos had been culling many worlds.

A number of their off world contacts were very angry with them, thinking that they had abandoned them to Wraith, many still thought of them as the Ancestors of old, others thought that they had merely saved theirselves, the teams had been forced to explain that they had been forces to return to their own Galaxy but they were back now to help the people of the Galaxy.

The Gate within Atlantis had seen constant traffic, with the teams returning to get trading supplies and returning to continue relations. The 'gate itself had changed back the moment the sensors had finished their sweeps of the Lantean Systems, and detecting that they were back in the Pegasus Galaxy the automated system changed the gate model again, it had also taken some time for the gate to calibrate for their new location but It was made easier as they had been here before.

John stood at the window of what was now his office looking down at the activity that was going on through the gate room and operations, he smiled only three hours in and Atlantis was reintegrated itself back into Pegasus, Woolsey had been sent to the Coalition with an escort, but as a matter of precaution he had also sent a second team as back up in a cloaked puddle jumper, he didn't expect the meeting to be entirely friendly but he was sure that in their absence the Geni would have tried to fill the void they left.

The gate lit up with an incoming wormhole but the kwoosh was stopped by the shield.

He saw that the technicians looked surprised so he walked out to operations to see what was going on.

"What's going on?" he asked

"Nothing Sir, Doctor Becket is taking his time getting through the gate." Chuck said "Teyla is coming through."

"Well lets roll out the welcome banners" John said smiling and he walked towards the stairs just as the 'jumper came through and began to ascend to the jumper bay.

When he arrived Becket was just managing to land, and the rear compartment door was lowered and for the first time in months John got to see Teyla. Her clothing had returned to her Athosian style and she looked good, on her hip was a small child that could only been Torren who had grown a lot since he had last seen the boy who had been named after John.

"John!" Teyla said warmly and embraced him carefully to avoid squashing her son, "it is good to see you again, I had not thought to see you or Atlantis back in this Galaxy."

"It is good to see you Teyla, and Torren too" John said and he tickled the little boy, "Lets just say that I did not agree with a decision so I may have taken the city without the full approval of Earth."

"You stole the city?" She asked shocked

"Not entirely" John said shrugging "Doctor Becket do you need anything?"

"I wouldn't mind some medical supplies, a number of the Athosians could use some of our treatments, but mostly they are in good health but I would like to give them a thorough going over and set up a small clinic for a day or two."

"That's fine, Where is Ronon?" he asked looking for his large friend.

"He said that he wanted to see how his people were but said that he would return to New Athos in a few hours" Teyla said

"Okay" John replied "Becket get back to New Athos and see the people. Now Teyla why don't we go downstairs."

They walked back down to operations were Teyla was met happily and it took half an hour for them to get into Johns office where she caught him up on the local news and rumours that she had heard. John also told her how the city came to be back in Pegasus and that he was now in charge of the entire city and expedition.

"John you are a good person, you will make a good leader to your people. Elizabeth would be proud if she could see you now."

"Except that she is now floating in the harshness of space and is unable to do anything" he said bitterly "have I told you how much I hate the Asurans?"

"Many times" Teyla said smiling "I noticed that you have also received a promotion in Rank as well, you are full colonel now."

"Yes, but I am not sure what my rank will be if I am brought back to Earth tomorrow." John said shrugging off the compliments "But I am the highest ranking military officer but it doesn't matter as I am still the leader of the Expedition."

"So what is your plan for this Galaxy?" she asked.

"Well I will be consolidating for the time being, and when I have my intel I will be able to plan the strikes against the Wraith but for now we have been gone too long to do any good, not to mention without the Daedalus which should be on its way our recourses are limited" he told her before adding "But I do have a proposition for you"

She waited patiently for him to continue and didn't interrupt.

"The Athosians were once welcome on Atlantis and the main land, I would propose that this continue. You told me that your people have struggled, and that many worlds fear you as they heard rumours of what happened with Michael. In exchange we will give your people protection and you will get the benefit of our medical treatment and housing that we will help you build on the mainland. in exchanged all we would need is a small amount of the harvest that your people would grow, the rest you can trade trade off world, you will also have use of the gate."

"What about security for my people and trade?" she asked concerned for her peoples wellbeing.

"Like I said we will provide your people with a settlement and means of protection on the mainland, I understand your people are a trading people, you can have full access to cultivate the land, however we will soon have three new vessels which we can teach you to pilot and you can continue your trade." John said smiling "they are not unlike the 'jumpers, they are easy to pilot and they will enable your people to trade easier."

"You are giving us your vessels?" She asked surprised.

"No" John said firmly "but they will be able to have use of them when they have need of them, but if needed they will form a military function. Primarily they are for transportation."

"I think my people would find that acceptable, but I fear that many will believe that we will be forced to relocate again." She said sadly.

"No" John said firmly "I give my word that the Athosians will always be welcome on Lantea, and in the city. The villagers can either remain farming and trading but some can if they choose join the Atlantis Reconnaissance teams or become part of the security teams."

"Might I also request a form of schooling for my people, many still do not have a true understanding of the technology or sciences in use." She requested ""I myself sometimes do not understand"

John looked thoughtfully "I think that can be arranged. We have enough geeks here to be able to teach your people something."

"You are kind to consider my people like this, I know that Dr Weir had too hoped to keep our people together but your people on Earth treated us with so much caution." She pointed out "will this not happen again?"

"No" John said firmly "I will not allow it, especially when your people were stolen without our knowledge. I promise you that even when we are back in contact with Earth, you and your people will not be forced from my city."

"Will they not just send a ship to find you, or even dial the gate?" Teyla asked after a number of minutes trying to settle Torren.

"Rodney is looking for all subspace transponders and locators, So no ship will find us, even if they send one the city Cloak will prevent our discovery, even the Asgard technology cannot detect this city." John explained "the gate has been programed for now to prevent any intergalactic dialling, but even if they do connect they will not be able to come through the shield."

"Well I had better get back to my people" Teyla said and she placed Torren in Johns arms "Please can you look after him until I return, I believe that on your planet you would be called a god parent to him."

John gave an almost terrified look at the small child which made Teyla laugh ash she left them, John looked like he was carrying a small bomb.

SGSGSG

A week after the meeting between Teyla and John, the Athosian's had all been transported to Atlantis where they received follow up care from the medics before they had been transported to the mainland to get a start on developing it for their new home. The previous settlement had been entirely dismantled and destroyed so they had set up a new tent village and the Athosian's with the man power of Atlantis began to get things back on track. The farmland that had previously been fruitful had become vastly overgrown and full of weeds, so the teams of farmers had got to work on that immediately.

Designs had been settled on by John and his senior teams for the new settlement that they would build on the mainland for their new society, and they had drawn heavily from Atlantis and the Atlantis Database for inspiration for the design. Housing would consist of buildings three stories in height that contained six flats. They were using a stone called melonite that was unique to the Pegasus Galaxy, the stone was enriched with a metallic element. The metal element contained within the stone was slightly weaker than refined trinium but it allowed the stone to be welded together rendering cement obsolete. It was hoped that the settlement would last many centuries and they designed them to be as ageless as the great city itself.

They designed the settlement with efficiency in mind: Heating was supplied via geothermal energy, lighting was powered by solar energy with Additional power to be supplied by naquadah generators. Under the settlement a series of maintenance tunnels where all utilities ran began to be built, they planned on recycling all waste products and a water treatment and pumping station but they did not currently have the means to build necessary facilities.

Water and waste disposal was taken care of on Atlantis, all waste was transported to the city to be processed whilst water was shipped to the mainland from the cities water treatment facilities. It was not an ideal situation but they made it work with minimal fuss, and the Athosians were happy with all they were doing and were keen to help.

The stone was sourced from a nearby planet and cut using laser saws before being transported to Atlantis, in the week since work had began they had only managed to build two of the tunnels and started work on one of the residences. The schooling that Teyla had requested had also been agreed and two larger tents had been erected to begin the education of the Athosians, they started two schools one for children and one for adults where they could learn new skills and science if they so chose.

The Coalition of Planets had not been welcoming, Woolsey had reported, they had believed that they had stolen the city of the ancestors and abandoned them all to return to their safe galaxy far away from the Wraith. Woolsey had patiently explained the reasons behind the necessity of the city's temporary relocation, and told them that they were now here to stay and would begin to confront the Wraith. A number of the members had not been impressed by their story but it had been the Geni who had questioned their integrity the most, which of course was for their own gain.

It has taken some stern words from Woolsey to stop their persistent questions, but the nail in the coffin had been informing them that Atlantis had been built on Earth, the Ancestors had come from Earth and returned to Earth after they fled and that they were the were the children of the Ancestors. The Coalition had stooped their inquisition and they had turned to other issues that they had and updated Woolsey on the news of the galaxy.

John had been pleased to see that Woolsey had taken well to his reviewed position he even had a new office, John had delegated some additional responsibilities to him like helping with all personnel issues but John still oversaw everything he did. Woolsey seemed to understand why John had gone about things as he had done, he just did not agree by the means he achieved it.

But John also knew that military commanders did not last long as leader of the Atlantis expedition, the expedition was sponsored by an international committee and they would want a civilian in charge not a member of one nations military. A military commander would not last long as leader of the expedition; the international committee that sponsored the expedition wanted a civilian not a military man. John was trying to be as accommodating as he could be to people of all nations and tried to not to favour the people from the US.

However the most startling discovery John had been made aware of was one that had become a mystery and something that no one could explain.

A young graduate called Gordon Matthews from England who had been sent by the British Government to be a part of the expedition, he had one of the most gifted minds known to Britain, he had drawn the attention of the government who had given him clearance to know about the Stargate and study advanced science theories and applications.

He had been searching through database when he had found traces of a program that had terminated on their return to Pegasus, on further investigation he had found that it had been a virus that would have destroyed the Atlantis Database if the city had not returned to Pegasus within another three months of when they left and had brought it to the attention of John directly.

"Rodney how did you not know that there was a deadline?" John asked in an emergency meeting.

"Well it was a buried program, the moment the city settles onto a new planet the sensors immediately sweep the planet and surrounding system, the city would have recognized its system of origin and I would imagine that this virus initiated in the background, it may have even have started once the city crossed over to the Milky Way."

"Sorry Doctor McKay" Gordon said nervously drawing attention to himself where he had sat silently, "You are not wrong in what you are saying about the city, but I checked when this virus was created, it was created four days after the city landed, when the first talks of the destruction of the city were proposed formally."

"What?" Rodney said taking the young lads tablet to check "He is right, it was created after we returned to Earth."

"This was a good find Mr Matthews" John said acknowledging the graduate "You have shown you are quite able to search through the database, please continue to do so and see who entered this virus into the system."

"Yes of course Colonel" Gordon said blushing "I will get right on that."

Once he was out of the room John looked back at Rodney, "Is it possible that that virus couldn't have been planted into the database?"

"No, there are protocols in place that would have prevented it, to make amendments to the database requires the key of the leader of the expedition and senior members, and there are Lantean security measures written into the very foundation of the database that would prevent viruses being planted into the system." Rodney explained "Even if someone uploaded the virus they could get it into the operating system but it would never migrate to the database, not as far as I know, It is like someone knew exactly how to bypass the security protocols and write it into the very base code"

"Rodney, You will need to allow Gordon more free time as i want him to comb the database for more information, I want possibilities on how this virus was installed into the database and by who." John ordered "Now Gordon please excuse us we have a senior meeting that i am bringing forward since we are all here."

/*****************************\

So the Athosians are now once again part of the city.

The next chapter will bring another part of the Lantean Society to the city.

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	5. Chapter 5

**Chapter Five**

**Last members of Lantean society**

In the two months since Atlantis had returned, they had resumed their off world trade and were beginning to settle in, but they had also resumed their campaign against the Wraith. John had been forced to release Todd after he had somehow managed to grow a Subspace transmitter in his own body, they had brought him to a planet where a culling had destroyed the entire village. Todd's former alliance had tracked him and they had handed him back, they could not just keep him in stasis, especially if it would give away their location.

John had warned him that if their paths crossed or they heard that he was feeding on human worlds then they would hunt and kill him, no matter if they had been allies previously, Todd had seemed to expect nothing less and had agreed and left via the planet stargate. Todd's lieutenant had given them more information on the Wraith: Three Queens had allied themselves and had begun to dominate the Wraith under their will.

But John knew more than Todd's alliance, he knew that the Trinity Queens as they were called did not currently have the needed ships to spread across the galaxy. But there was rumors of a small planet where they were growing a new fleet. Todd had managed to locate it on his own and had traveled to a planet that he knew Atlantis monitored, the planet was on the outer rim of the Galaxy and off the gate network, But he had not found the exact location but John had knew that it would take months to find.

The _Daedalus_ had arrived and with it came three cargo vessels named CX:600, they were specially built shuttles built to support Earth and its assets. They had been designed after the Puddle Jumpers had been studied. They had a cockpit like the 'Jumpers but the controls were not like the jumpers but it could be seen that they were influenced by them. The rear compartment was three times the width of a Jumper but the design was curved and the ships had wings.

They cargo ships were built with two methods of transport for cargo: Ring Transports and a modified Beaming System that could not be used on weapon signatures. The shielding came from a Starfighter Shield generator that had been developed for the F-302's, its interstellar hyperdrive was Earth designed but its technology was based on Goa'uld drives but had been created from scratch using the superior knowledge of the Asgard and Ancients to maximize its output. It was equipped with weapons: two forward facing rail guns, but on the belly was revolving turret that could fire plasma bolts but would use up considerable power.

As promised John had began to allow the Athosians to learn to pilot the ships but it would be take many months before the were fully capable of independent flight, so that an Atlantis pilot would accompany them at all trips, but they would also be required to operate the weapons systems. A further precaution was written into all of the systems, a Bio-metric relay that would only allow keys people pilot the ship and even activate systems.

John decided that the Alpha Site would be located on the Planet formally known as New Lantea which they had renamed Tanair. Work had already begun on building the underground facility, it was difficult as the planet did not have a stargate which meant they required the _Daedalus _to transport materials and engineers to the planet. Another issue with the planet surface was the native venomous snake creature which made the project problematic but they were able to work efficiently.

They used the _Daedalus _plasma beam weapon to excavate a hole into the planet surface and the teams had begun to work on the rest of the facility using laser cutters that Jack had transferred to Atlantis as part of their supplies. John had the engineers working on a shielding system that would prevent detection from orbit, he knew that if Earth sent a ship after them the first places that would be searched would be both Lantea and Tanair.

Once the shielding systems were working and installed and the Gate room completed a Stargate would be installed to help with the work, the _Daedalus_ was not always available which slowed the work considerably.

Atlantis's new society was not yet completed, John had one more race of humans that he wanted to locate, and that meant he needed to leave the city for a while, and there was only one person he could leave in charge temporarily.

Teyla. She was not often off-world due to being a mother, which meant that he could have her stand in for him temporarily, it was a role she had undertaken a number of times which made it easier, but it was the respect that she had from the people that allowed her to fill in for him, She had Lieutenant Colonel Lorne to help her with any military emergencies, and Caldwell could manage himself whilst John was away.

With the city in safe hands he took one of the cargo ships and went out in search of the elusive people who nobody had seen or heard rumour of since Atlantis had left this galaxy. It had taken a week of searching known locations of trade for John to find a sign of them and the people of the planet were being very odd, so he left them a communicator and left the planet.

He was on his way to the next planet on his list of possible locations when he received a transmission from the communicator he had left.

"Sheppard, I hear you are looking for me" said a female voice

"Larin are you hiding from me?" he asked with a smile knowing how much she liked to antagonise him.

"What do you want Sheppard" she asked in a bored voice

"To talk, we have been gone a while and I wanted to reconnect with my friends" he said carefully.

"You have been out of this galaxy for some time, the Wraith have been culling worlds again with no one to protect them, we have been hard pushed to survive, three of our ships have been damaged heavily in fights." She said sounding angry.

"Well then, I think you will like what I have to say." John said and he opened up a program and raised a long range communication channel to her, "I will send you the location of Atlantis, meet me there and we can discuss something that will benefit the two of us."

"Fine, I will be there in three hours" she said and ended the communication.

John couldn't help but smile to himself, she was a very powerful and formidable women and he couldn't help but like it.

It took just over two and a half hours to get back to the city, he landed the ship onto the east pier where the Tria was still docked, the scientists were working every day on the ship but the hyperdrive was incredibly damaged and the reports he had received had shown that it was near irreparable. They were making headway, they had originally wanted to learn from the ship and to reverse engineer its technology, but since they now only had one ship he decided he wanted it operational in case of emergencies.

All systems other than the hyperdrive were operational, but its arsenal of drones was nearly entirely depleted, they had discovered that the ships had two further weapon systems. The First was the anti-fighter turrets that were hidden under the hull that would deploy once initilaised, the weapons were self tracking and firing but were more advanced that any the people of Earth had currently.

The second weapon was ship variant of the Ancient beam weapon that they had found installed on Atlantis and in the weapon satellites that had once defended the Lantean system. The weapon had been named the Groddin Weapons Platform, after the British scientist who had been killed using the satellite weapon. The weapon was superior to the Asgard beam weapon, and preliminary tests suggested that these weapons would be able to cripple even a Asgard O'Neill class vessels.

The downside to the weapons platform was that it required a ZPM, A Mark II naquadah generator could power the weapon but it would take twenty minutes for the necessary power to buffer for it to fire, with a ZPM installed it could first rapidly since the ZPM could give the necessary power immediately and without the need to buffer. The Groddin weapons system was being researched in the Atlantis Database by Gordon, John hoped that he would succeeded where McKay had failed, he had only been able to find the description of the system and instructions on its use, what was needed was the schematics.

One technology that there currently developing with success was the Control Chair. Earth no longer had a chair to operate the Antarctic Outpost, the Wraith had destroyed it in their attack, if they built one it would go a long way in mending fences with Earth when they re-established contact.

They were making great strides with shield technology thanks to Atlantis and Tria, but the _Daedalus_ had brought them knews of the Icarus Project and the _Destiny. _The Altera were the first to create shield technology and were the most advanced in the known universe: the most powerful of their shields were the City-ship variant that were impenetrable as long as it had sufficient power. Their second variant has been used by their ships, they were given shaped shields that contoured around the hull, they allowed for better velocity speeds and protection.

He knew that when Larrin saw the ship she would attempt to bargain for it, but he would cross that when it came to it, and he had no intention of that ship being used by anyone yet, once back in Stargate operations his attention was called.

"Colonel Sheppard" Chuck called, John walked over to see that he was looking at the long rang sensors.

"I take it we have a visitor?" he asked.

"Yes, we have been following this ship, it has been following your heading and will be here in twenty minutes, but the system is recognising the vessel as a Traveller Generational Ship." Chuck said "is that who you was looking for?"

"Yeah" John replied "the Athosians are cultivating the mainland providing food, trade and soon they will begin to develop again as an advanced race, the Travellers I hope will be one of our allies."

John didn't explain further, but walked back to his office and pulled out a folder with information he had been preparing for this very meeting, Zelenka had the most knowledge on their ships capabilities and had proposed a number of upgrades that they could provide them.

He set up the briefing room for the meeting, gone was Woolsey's monstrosity of a desk, instead they had brought back the Atlantis high council seating. Waiting was Rodney and Zelenka as the scientist who would carry out any possible repairs and upgrades, Woolsey who handled all negotiations and diplomacy and Teyla and Doctor Keller.

When the ship arrived it took them ten minutes for them to be escorted to them meeting room and she looked eager for the meeting, but happy to see them again.

"Shall we take a seat?" Woolsey said and indicated to seats on the other side of them.

"I was surprised to hear from you Sheppard; we believed that you had abandoned this galaxy." Larrin accused him cutting through the diplomacy.

"A Wraith vessel had powered itself up using a Ancient power source and had managed to locate our home planet in another Galaxy. We were forced to return to protect our home but our place is here in Pegasus. " John explained "I got the city back here so that we could continue our fight with the Wraith."

"What does that mean for my people?" she asked with interest "Why am I here?"

"Colonel Sheppard is in command of our expedition, and he has the following proposition for you and your people. We would ask for the support of your ships in the battle against the wraith" Woolsey stated "in return in the spirit of co-operation and a show of good faith, we are willing to repair your ships and remove the many years of patches and cannibalism of the systems."

Larrin's eyes brightened "That is quite the proposal, but for us to even consider we would require the Lantean ship that we saw docked on your city."

John smiled to himself at her predictability.

"Unfortunately the vessel you speak of is not part of our deal." Woolsey explained firmly "That ship is not operational and will not be for some time, however if you agree we may be able to share any advances that we make as we study the technology."

"What will you wish of my people?" Larrin asked "Most are not soldiers or even technicians."

"Your ships will need only crews to operate them efficiently, the ships of course will remain the property of the Travelers. The remainder of your people will be free to make use of the mainland and here on Atlantis. Your ships will be used to act as support for the _Daedalus_ and the city." John explained the proposition further "I will also help your ship crews by stationing some of my own people under the command of your captains. We would like to count on you as allies in our fight and to fight shoulder to shoulder with us."

Larrin sat quietly; her two officers remained silent deferring to her as captain of the ship.

"As you know I am not the leader of my entire people, I cannot make this decision without speaking to the other captains, but I will take this to them." She said careful to avoid making a mistake, "This sounds good and is fair to my people, but your plan risks our ships, they not only keep my people on the move and safe,they are our homes. I cannot risk the ships or endanger my people"

"Colonel Sheppard offered you the use of the mainland here and the city." Woolsey pointed out, "It would not be the first time in recent history that you have colonised a planet."

"As you know our first attempt in centuries ended with the destruction of the Stargate and destroyed our own Lantean warship." She pointed out eyeing them up, "something that your people could have prevented if you had stopped those race of humanoids."

"Larrin my own people are already settled on the mainland and we would welcome your people as neighbours." Teyla said "My people are farmers and traders, but we are protected here on Lantea."

"It could work" said one of the officers, "Our people would be safe whilst we fight the Wraith and our population could grow."

"It could" Larrin said and she turned to Doctor Keller "Would we have access to your medical staff?"

"Yes of course, you would have full access to our medical care either here in the city or in the clinic that is being set up on the mainland." Keller said "But we could also teach your people medicine, I do not know your current knowledge but if there are gaps we can help."

"My people have also begun to be taught by the people of Earth to further our understanding of the universe, Your people could receive further learning, you knowledge of science is higher but they might be able to offer you more." Teyla added, John knew that she was happy that her people had embraced the new way of life they were being given. She and Kennan were joint leaders of her people and both had noticed that the Athosians were much happier even if their relationship was strained slightly.

"I think we can agree, but it would be dependent on the disclosure of further Lantean technology, but we have needed new ships for three generations, we would like to be able to build some new ones."

John sat silent, he had not expected that demand, but there was merit in it.

"We do not currently have the resources to build a shipyard, but we too have the same need." He said "Once the mainland settlement is completed we will begin to build the shipyard, but we also need to finish our safe world facility too. However things will go much faster if we have your peoples help in construction transporting, and mining of raw materials, which would mean that a joint shipyard would built sooner. The mainland will also serve your people so you should see that as good reason from delay. Your request for Lantean technology will also be honored, especially as you will have access to most of our technology which we develop, as you will be a part of Lantean society."

"This alliance has potential for both of us." Larrin said in agreement.

"You should know that we currently cannot replicate or produce the Ancient technology, we understand it and some of the science but production of the technology is currently beyond us." Zelenka said quickly"But if we were to build a facility for ship building we could offer more, but it will take time to reach that aim, but for now this is what we propose to do to your ships"

Rodney and Zelenka went through the presentation explaining what they would give them, they planned to repair all hull deterioration, new power conduits and improve their hyperdrive technology with upgrades to the system and the hardware. But they would also overhaul most of the ships current systems.

"I would also point out that with the majority of your people on the mainland and in the city, this will free up space for cargo hold for the construction materials. But will allow more space of power generation and other technology." Rodney finished.

"For your ships to be fully up to our standards we will need to install a transport technology. Beaming technology is not on the table as that is technology we ourselves were gifted by a the race known as the Asgard. But we can install Transport Rings which are also capable of transporting matter between two sets of rings. But as I said our technology is loaned and will require one of my people on board to operate. But like I said before your captains would remain in command, we would only be there to help." John said quickly knowing that their ships would need some of their technology but he wasn't giving it freely and he wouldn't allow them the most current models or any of the Asgard systems "then if we give you any further technologies we will still be at hand to help and make sure your crew can use them."

"I will speak to the other ship captains" Larrin agreed, "But whilst I agree with this plan, they may not."

John nodded and they shook hands and they were escorted out of the city back to their ship and Atlantis hoped that they had gained another ally.

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Will they agree?

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	6. Chapter 6

**Chapter Six**

**Earth Comes Knocking**

A year had passed since Atlantis had returned to Pegasus, or more correctly since John Shepard had stolen the city. In that time the Lanteans had grown their infrastructure much like their ancestors had millennia years before.

The Traveller captains had all agreed to Johns terms and all of their seventeen ships had come to rest on Lantea where the Atlantis scientists and engineers had been set to work on them. Each of the ships were in different amounts of disrepair and to date they had only been able to repair five, but upgrades were slow to install as they lacked all of the materials.

The settlement on the mainland had grown quickly with the additional manpower and transport of the necessary raw materials, they were still building but over half of the Travellers and Athosians in the new homes. As Teyla had promised her people had welcomed the nomadic people just as they had welcomed the people of Earth so long ago when they stepped through the 'gate to Athos.

The people who had chose to live in the settlement were people with families with young children or the elderly, but other young people were receiving training with Ronon for Atlantis missions, some would be assigned to AR teams or even on the _Daedalus_. The five repaired ships had been put straight into service by John and they had begun guerrilla warfare on Wraith ships with the _Daedalus_ so far they had destroyed three hives and seven cruisers but there were being careful not to be caught by surprise, he remembered what Rodney had told him of what had happened in another timeline and he would not have the ships ambushed.

The remaining Traveler ships had been grounded around the settlement whilst the others were engaged in battles, transport and scouting. They were left on the ground to power the shield generators that they had installed in case they were attacked.

The only ship that had entered the Lantean system had been from Earth. The USS Apollo had been sent in search of them and the _Daedalus_ but since they had removed on tracking systems from the city and the ship they were searching blind. They had detected the ship via the long range sensors, they had wondered if it was a Wraith ship but when they saw that it did not drop out of hyperspace at all they realised that it was an Earth ship. As a precaution John had the city submerged to the ocean floor and activated the shield and set the city to slumber to prevent their detection.

When it entered the system it had lingered whilst they scanned the planet for them, but John knew that they wouldn't be able to. The mainland shield had been changed into a cloak using a jumpers cloaking system through the shield emitters, it was powered by all of the Generational ships, all of which were needed to prevent the Asgard sensors from penetrating the cloak or picking up the Generational ships.

John was not sure what state Earth politics were in, but until O'Neill made contact he would remain silent. The members of his expedition supported him and he did not hide from them that what he had done had not been sanctioned but what they were doing was in the best interest of the Pegasus Galaxy and in the long term, Earth. He had even taken the precaution of having Woolsey drugged to prevent his interference.

The Ship had stayed in orbit for a day, all gate activity had been suspended and the gate deactivated by blocking the event horizon. The ship had not beamed anyone down to the settlement which was fortunate as the cloak would not prevent them walking through barrier. It had eventually left Lantea after failing to locate them so they resumed usual gate activity and the city was returned to the surface of the ocean, but as a precaution all off world teams were ordered to take two or three gates before returning to Atlantis.

They had discovered that the _Apollo_ had remained in Pegasus when it had dropped out in hyperspace above the _Daedalus_ whilst it was in the midst of a fight against four hives on a lone mission where it had scouted the Trinity Queens territory. The _Daedalus_ had wanted to board the ships for data on the Queens but with Colonel Ellis in the area he had fled as quickly as possible to prevent a battle and tracking. The _Apollo_ had been engaged by the remaining ships and had been unable to track the ship but they had seen them.

On an unoccupied world they had found seven replicators suspended in a force field that had broken the moment an off world team had found them. They had been dormant and unresponsive until doctor Becket had touched one of them to check for life signs and they had awoken, they had been initialised by the ATA gene and their programming had been to destroy and attack. The planet that they were on was a previous Lantean outpost where the Asurans had been studied by a Lantean scientist without the knowledge of the council.

AR team 3 had been forced to run as they had not brought an ARG with them, and they could not stop the Asurans from replicating using the small deposits of neutronium and they had begun to build an Asuran cruiser. For fourteen hours the team had been forced to survive on their own whilst they waited for the Daedalus, the gate had been guarded by the replicators and they were unable to get past. Eventually the Daedalus had arrived and had used a improvised Anti Replicator satellite built from a ARG by Rodney and Zelenka on the way and they had been able to kill them all, including the replicators that were mining resources in the planets crust.

The Planet however became a new outpost for Atlantis with is supply of raw materials it was a good find, but they had found the remains a old mining facility that had been abandoned by the Lantean during the war with the Wraith, and they had taken most of the technology away but some still remained which they were able to utilise.

One Battle had been fought in the first year that had dwarfed all others, they had found a Wraith outpost accidentally and had discovered that it was an outpost for breeding and weapon research. The Trinity Queens had been found in orbit with their armada guarding the planet, thirty Wraith Vessels but Atlantis intelligence knew they had more.

The _Daedalus_ and six Traveller ships had run attacks on the planet, they attacked in waves destroying a number of ships before jumping back to hyperspace, before returning and repeating the same tactic. It had been a hard battle but they had won, forcing thirteen wraith ships to flee to prevent the total destruction of the fleet. The Atlantis fleet had not been unscathed, one of the Generational Ships had been crippled and the Daedalus had suffered an overload in its APB weapon systems, but they had been able to return to Atlantis with the Traveller ship in tow.

The planet had been scouted by teams, and they found that the facility had been booby trapped, they had lost a large number of ground troops and two jumpers in the traps, But they had discovered that the Queens were developing shield technology. Most of the Data had been lost or corrupted but it seemed that they had made partial success with their research and Atlantis feared that the Wraith would no longer rely on their organic hull and armor.

John was standing out on the balcony overlooking the city that was now under his control, it was still strange to think that he was in command of this great city and its people, even the Travellers and Athosians now looked to him as their leader. He did not overly enjoy sitting behind a desk, but the situation had called for it and he thought he had done well, Sometime he thought he could feel Elizabeth looking over him, guiding him and he wondered what she would say if she was still here.

He knew that the merging of three separate cultures was made easier with the single goal, but over the year and relationships had begun to emerge and they would be welcomed their first Traveller-Tau'ri child to the world within the next couple of months.

Many in the Pegasus Galaxy referred to the people of Earth who resided on Atlantis as the Lantean's, but the new society now fully embraced the name and took it as their own, they were one people now under a single name. The leadership of Lantea and the city was made in the image of the Ancients who had called the city home, the New Atlantis Council had been formed.

John was the High Councilor of Atlantis as Leader of the Expedition, Larrin had been appointed by the Travellers to represent them in all matters, the Athosians were jointly represented by Teyla and Kenan. Rodney and Jenifer were also on the Council as Head of the Science Division and Chief of Medicine. Evan Lorne was the military leader on the council, with Caldwell representing the _Daedalus_ crew. The final seat was taken by Richard Woolsey who oversaw trade agreements and diplomacy but also to keep everything on record for the IOA when they could contact Earth.

And they did not have to wait long for that moment, only a week after the councils formation they received an unscheduled activation of the Stargate.

"What have we got?" John asked eagerly, The strain of command was starting to weigh on him and he felt cooped up on the city, he needed to get off world and fight on the front lines. He couldn't understand how O'Neill could stand it, after all his years as leader of SG1.

"Incoming wormhole" Chuck said reading the screen in front of him for the IDC, he paused and a look of shock appeared "it's from Earth."

John sighed; he wondered what the IOA would try this time to bypass the shield.

"This is Commander Jack O'Neill of Homeworld Command, Colonel Sheppard?" said a voice over the radio frequency.

John didn't want to trust the transmission, replicating vocals was easy with the right technology.

"Sheppard, I told you that when it was safe I would call and that I would tell you that even in command it is possible to find those that you want to spend your life with" the voice said " I also know that you have used some of your own money to pay for the resources you took with you, and I helped you with your plan."

"This is Shepard" John said patching himself through onto the channel, "How can Atlantis help?"

"The IOA has finally relented on the issue of the city leaving Earth and we can reopen channels between us both, also I will be sending the Apollo as part of your support fleet." Jack said "The IOA will want a full report and representative on board"

"No need General" Woolsey said stepping forward "I have been kept here since the city returned and I have kept an account of our time here, I will report to the IOA but I believe that Colonel Shepard should remain in command."

John had not allowed anyone through the gate, instead he had insisted that Atlantis dial them back. He had sent Woolsey alone as he would need to speak to the IOA and John did not feel safe just yet going back himself.

Two days after O'Neill had dialed in, Woolsey returned with General O'Neill and explained to John that their relationship with the IOA was strained and would be turbulent going forward.

O'Neill had explained that the issues had been resolved faster because of the problems with the Lucian Alliance and the Destiny Expedition. He told Sheppard the resources that were being spent were being channeled into ship production as the Alliance was attacking worlds they protected and there was evidence that they had infiltrated Earth.

The one niggling issue the IOA had with his leadership was his formation of the new Lantean society they had wanted them all removed and replaced with Earth citizens only, a number of the nations who made up the Expedition Supporters had not minded but the IOA was trying to get their foot in the door.

The IOA had insisted on an intensive audit of all Atlantis operations and they wanted to screen their entire staff of off world members. John had agreed to the screening but had told them that they could speak to the senior members, but for the ordinary citizens he had insisted that either Larrin or Teyla had sat in on the interviews to relieve their people's tensions.

The city had seen an influx of people with high ranking members of the IOA, members of the SGC and governments from Earths nations arriving, but they received a constant escort to prevent them from doing anything to harm the city.

Since they were an entire galaxy away, the chain of command was very blurry and it was difficult to comprehend that they reported to Earth and Homeworld Command, John tried to walk the line but it came as a surprise when he realised just how different the running of Atlantis was to that of Earths many governments and he realised they didn't really fit in with it.

John had left Pegasus after the evaluation and visited Earth with General O'Neill after he had been promised that he would not be prevented from returning, But he had ordered the Daedalus return to Earth just in case.

When he arrived he had been met by the President who had wanted to meet him, and had received his promotion to Brigadier General from him, but was told that the IOA have fought against his promotion. John had planned to leave Larrin in charge of the city, but she had asked for the opportunity to visit Earth to see his home planet and the origin of the Ancestors so Teyla took charge.

Larrin was awed by what she saw; It was a culture shock, especially as there were no civilisations in Pegasus that could rival Earth. The population density was what shocked her, but also the diversity in culture. John took her to Area 51 to see the R&D and took her to their shipyard where the BC:304 Elizabeth II was being built.

To ease relations between Atlantis and Earth they presented them with a new Control chair that Atlantis had built, it was not dissimilar to Ancient model but it was obviously Earth technology, and it had been transported to Area 51. With the connection back to Earth and further resources the Settlement was completed and its facilities finished, they also finished the Alpha site installation. New advances were also to be shared, Rodney was able to finish the the Subspace capacitor which had been built at Area 51 that had a number of faults.

Gordon Matthews had found a number of entries into Atlantis database that had been added spontaneously with no reason and nobody had entered them, he had not found who created the virus but whoever put it into the database had bypassed every security protocol.

He did however find a reference to an Lantean docking port that was built to help the city and to prevent their ships falling to wraith hands in the resource outpost, its location was not known but it stated that the transport shuttles that were once on the planet had been sent to the port when the Wraith arrived. He had also found records of another facility that sat in the power of life to bring great power to the Lanteans, but it seemed that the all exact references had been deleted from the database, but the vague reference was one of those files that had been added by the unknown person.

The young boy requested leave from Atlantis for a time, he wanted to study the Asgard core under the observation of Doctor Jackson who was stationed on the Odyssey, John was reluctant to let him go as the boy had a knack for finding information but he also possessed a powerful ATA gene aptitude but John agreed but made him promise to return.

/*****************************\

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	7. Chapter 7

**Chapter Seven**

**Death in the library **

Three months on since Earth and Atlantis had reopened communication, John was still in command but the scrutiny that he was under was increasing and John could feel himself cracking under the pressure, The Wraith were trying to strike at them by attacking planets they traded with which had caused the Lantean fleet, small as it was, to be spread thin.

John had wanted to go off world to help the people they traded with or even look at the damage with his own eyes, but he had been forced to stay on the city even when the other council members could travel as they pleased. The IOA were looking for an opportunity to replace him and if he left they might attempt a coup, or at least that was what Woolsey had told him.

It amused John to no end that Richard Woolsey, the interfering IOA placement who had come to correct the way the city had been run, had changed to the extent that he was now a trusted adviser even if John was still wary of the mans loyalty.

The IOA held little power over Atlantis, and recent news from Earth had John glad that they did not hold absolute power over the city. The Lucian Alliance had been able to locate the secret Icarus base where they had been researching the ninth chevron and had attacked them forcing the people on the base to flee through the gate to the _Destiny_. The Alliance had then found a second Icarus type planet and used Earth technology and research on dialing Destiny to tap into the planets unique properties and dial the _Destiny_ transporting a number of the Alliance to the ship to try to take over. launch a assault on the ship.

The Alliance's knowledge of their top secret projects greatly worried John as it meant that they had access to the top levels of Earth organisations and commands. Brainwashing technologies had been used in the past which meant that they could have sleeper agents passing them information and the person wouldn't even know what they were doing. But what had clinched the severity of the Alliance threat was the Tel'tak that they had crashed into the building with a seventy megaton Naquadria bomb on board. The bomb had been defused thanks to the Destiny Expedition but radiation had leaked and luckily only two people had died, but many suffered radiation poisoning.

If the Alliance knew about the top secret Icarus and _Destiny_, then he knew that they were aware of Atlantis. _Destiny_ was so very far away it was nearly impossible for them to attempt to board the ancient ship unless they found another suitable planet, but Pegasus was only one galaxy away and it would be seen as easier prey.

The Alliance used what remained of the System Lords fleet, and that meant they used a Goa'uld hyperdrive that was limited to interstellar travel, but if they were able to obtain star charts for Pegasus. John had considered it likely that the Alliance had acquired Earth hyperdrive technology or may have found a upgraded Class III Goa'uld drive designed by Anubis using knowledge from his ascension.

John's first thought had been to close all access to Atlantis from the Milky Way, both because of the Alliance and the IOA but he needed the communication to Earth and owed it to his people, and they needed supplies.

_Apollo_ was often used as their supply ship, and John made good use of it whilst it was in Pegasus using it to help take out the Wraith but they seemed to have disappeared, and were not appearing on the long range sensors but they had been made aware of a number of worlds that had been attacked.

Caldwell was the commander of the Pegasus Defence Fleet, when _Apollo _was in Pegasus it fell under Lantean jurisdiction, and therefore Caldwell was Colonel Ellis' superior. A fact that Ellis had not been happy about and when he had been told he had immediately had the gate dialed to Earth so that he could talk to General O'Neill. John has not known the exact content of the conversation but after Ellis had accepted his role on Atlantis and had complied with every order Caldwell had given.

When the _HMS Elizabeth II_ arrived at Atlantis John had been very surprised as he had not been made aware that it was on its way, but captain had explained that this was their maiden voyage to test the capacity of their upgraded hyperdrive over long journeys, it had made it two days earlier than other ships of its class.

The ship was one of the more powerful 304's having a new power source, the subspace capacitor, designed by Rodney and Carter and built by hundreds of technicians at the Allied Stargate Technology Development site, locally known on Earth as Area 51.

The capacitor was a marvel in Earth innovation, which Rodney was very proud as it had been his idea and he had been the leading mind behind his development. John however made a point to remind Rodney that he had cheated, having seen the technology on the alternate _Daedalus_ from another universe. However despite the odd origins the capacitor was planned to be installed on all of their ships eventually to provided unlimited power at larger levels than the current limited naquadah generators.

_Elizabeth II_ had not come without any supplies but they had come with another objective, they wanted to take a copy of Atlantis Database. Whilst the city had protocols in place to prevent it being transferred out of the city, a portion could be copied to an external drive.

The crew had been allowed into to the city whilst the supplies were transported and whilst the download was going through, the city security protocols had been updated to prevent the crew from getting to areas they were not authorised to enter.

Gordon was sitting in the Lantean library, a room that was located on one of the outer piers, it contained many database terminals but also a great library of books. The library had been found accidentally by a team of structural engineers who were checking for damage on the outer piers, the database had it labelled as a storage area.

The books had been damaged in the floods that had ruined other areas of the city, most were now illegible, some were salvageable and the library had also contained a number of stone carvings and oddities covered in Lantean carvings. They had also found some digital books which would need to be repaired to work but they hoped that the data could be salvaged.

Gordon was a very capable researcher, fluent in Ancient, Goa'uld and Asgard, knowledge retention had come easy to him since he was a child, but he occasionally dabbled in technology development, his pet project since arriving on Atlantis had been working on Lantean stun weapon technology but he still had far to go before he was happy.

He was sitting in the library researching the vague reference he had found to the Docking Port and the great power of the Lanteans. He had been unable to find anything and it was frustrating, he could find no hidden partitions or unauthorised access to the database that could have inserted the new data.

"This database has so many redundancies and security protocols, but this data has been uploaded into the back ups, but I cannot find any other references to them!" he muttered with annoyance and he knocked his papers onto the floor as he hit the table.

As he bent to pick it up he heard the door open

"Doctor McKay I will be out of here when the _Elizabeth II_ departs" he said in annoyance "I have already told you that I know my way around the systems and I will not break anything."

Choosing to ignore the brilliant but arrogant scientist he continued his perusal of the database, McKay continued to walk towards him but still did not speak.

Wondering why the usually very talkative man was so silent he turned, and it was only then he realised just how close the person was, dressed in Atlantis uniform, but it was not doctor McKay and he was walking towards him with a hypodermic needle.

"What –" Gordon said startled jumping to his feet as the man lunged.

"You were not supposed to be here" the man said casually "Not that it matters nobody will find your body."

They began to fight and suddenly Gordon knew no more.

John was sitting in his office going over the latest data when an alarm sounded, and he rushed out of his office

"What's going on?" he asked

"The City just set off the alarm." Amelia said "I have never seen this before."

"Radek" John said into the radio "Please come to operations."

"Yes Colonel" Radek said breathlessly.

John was not surprised to see the man only a minute later looking out of breath.

"Where were you?" John asked curious

"At grounding station four repairing the system the Genii broke." He said "What is the alarm for?"

"Well I was hoping you could tell me" John said "We have never seen it before."

Radek walked over to another station and pulled up the city systems diagnostics. "The city has detected a life sign that has disappeared on the outer edge of the city. But the sensors have also picked up weapons discharge!"

"Where?" John demanded

"The library on the south pier!" Radek said

"This is Colonel Sheppard to security teams, head to the library, we have detected a gunshot." John ordered "all security teams to secured areas" he added finishing the broadcast and turning back to Radek and Amelia "Secure the city, but allow the security teams through."

John left operations as quickly as he could and made for the transport booth which opened as he approached and pressed the closest booth to the library, but it was still a long distance to the library and he broke out into a run to reach the room as soon as possible.

When he arrived he was met by a sight that surprised him, lying unconscious on the floor was Gordon Matthews with a gun in his hand, but laying in a pool of blood was a man John didn't know with a gunshot wound.

"Sheppard, we found them like this, we cannot wake Matthews." A security officer said, who had been recruited from the Travellers "I have requested a medical team."

"Good" John said and he walked over to the dead man to get a look at his injuries: he had two bullet wounds, two shots to the heart, the kill shot for a marksman. he walked over to the closet terminal out of the way of everyone and contacted operations "Radek can you send me Gordon Matthews file to this terminal"

"Sure" Radek said and a minute later the file appeared on the screen in front of him.

The terminal did not have access to restricted information, like personnel records or security information but Radek could add it to the screen by some technical magic that John didn't want to understand. He had read the young man's file before, but wanted to check for something.

After five minutes of searching the files, Doctor Keller had arrived with a team of medics and they had wheeled Gordon to the infirmary. She bent down and examined the corpse.

"Don't tell me, death by gunshot?" he asked walking over to her.

"Yes, but he also had a broken wrist and two fingers." she said studying the man's body.

"You know I have seen these injuries before, but usually only by those who have had Special Forces training." John said frowning, the young researcher was very liked amongst the Lanteans, but John wondered how the man had managed to take down a man who was twice his size.

"Sir" a security officer said holding something, John turned to see what he had and saw he was holding a syringe "We found this under the table"

"Get that to one of the labs, get the substance analysed. Neon green does not like a vitamin shot."

"John he has these on him" Jenifer said, in her hands she held a set of data crystals that looked remarkably Goa'uld in origin.

John took the crystals and handed them to the security officer, "Get these to McKay and Zelenka I want these cracked for whatever data they have on them, Jenifer please see if you can find out anything more about our mystery guest. I do not recognise him which makes me think that he is not on our staff."

"He also not Athosian or a Traveller" Doctor Keller said looking into his mouth, "This dental work is from Earth, I also do not recognise him, but I would guess that he could have come on _Elizabeth II, _they have been docked with us since last week."

"True" John replied rubbing his chin where stubble was accumulating, he pressed his radio with a sigh "This is Sheppard, I want the _Elizabeth II _and its crew to be contained until further notice, I want the crew manifest and photo identification to be compared to the crew, we seem to have a mystery guest who will be in the morgue"

"Yes Sir"

"Whilst they get that going I think you should get to your patients Jenifer, I will assign a guard to the infirmary just in case there are more of them, But keep me posted when you find anything on the body or if Matthews wakes up, I have a few questions for him." John said, but he didn't get far before the captain of the British ship demanded to know why his crew were contained and what the situation on Atlantis was.


	8. Chapter 8

**A New Player**

**Chapter Eight**

It has been two days since the strange death on Atlantis; Gordon Matthews had still not awoken from the odd coma he had been found in after he had been attacked by a mystery assailant.

General Sheppard sat reading through the reports that sat on his desk, the entire crew of _Elizabeth II _had been quarantined and questioned and they were no further forward, the dead man had been on the crew, a late addition to the crew appointed by someone back on Earth. If John wanted more information he would have to contact Earth which was not something he was inclined to do.

The dead man who was called John Smith, which was a name which made John wonder how it had not been flagged. A full autopsy had not given them more information, cause of death was two bullets to the heart, but his wrist was broken as was two fingers on the same hand which John had known the day it had happened.

John sighed and pulled out a bottle of Aspirin from his drawer to try and relieve the headache that throbbed in his head, he had been in sessions with the council nearly all day. The Travellers were becoming divided; most wanted to remain with Atlantis whilst others wanted to continue roaming galaxy. Larrin's influence only went so far and she empathised with her people as they had known that way of life for so long but she had told them that they should stay, John knew that in the future some of the Traveller ships would return to their previous ways. So he made a plan to release two of their ships back to them to roam free but he would be keeping it secret for now as he didnt want their society to full apart.

The Athosian's also wanted to develop further, Teyla had taken a number of her people to Earth to visit the planet that had been able to develop without threat for thousands of years and what they had seen had shocked them but it had also given them ideas. The Athosians were a previously advanced people that had been reduced to a trading people down to mere farmers. With Atlantis now helping them return to stable living and they could now take the next steps in moving forward.

Teyla asked if Atlantis would help in rebuilding Athos, She had seen the markets on Earth and wanted her people to trade on a larger scale. They proposed a galactic market that would be opened to all planets in Pegasus, and they hoped to bring more worlds to into the coalition. They had begun to build the start of the market, it was basic but it would function well enough. They had spread the word that in a year the market would open and all people of Pegasus were welcome to trade their wares, they had decided to wait to give out the gate address but it would be sent closer to the time.

"General Sheppard" said a female voice over the internal radio.

"Yeah?"

"He just woke up, you might want to come down" Doctor Keller said in a tense voice.

"On my way"

When John arrived in the infirmary, he saw that Matthews was sitting up eating a bowl of what looked like gruel but look otherwise fine, but medical personnel were performing tests on him whilst he ate.

"General" Matthews said surprise "Doctor Keller will not tell me what happened to me! I was attacked!"

"Yes I know" John said watching him carefully "what do you remember?"

"I was studying the database looking for the information you asked for, the door opened and I thought it was Dr McKay checking up on me as he has taken to doing, it was only after he did not say anything for a number of minutes that I turned and noticed that he had a needle in his hands and I do not remember what happened next as all I know is I woke up here." he said glumly.

"Well I hope you feel better" John said lamely and walked over to Doctor Keller who was looking at a computer screen. "Have you learnt anything new?"

"No, as far as I can tell there is nothing wrong with him." Jenifer said frowning "His blood work shows no abnormalities and neither does his brain scans, his recognition shows nothing untoward. I ran a number of scans looking for signatures of the brainwashing technology we are aware of being used for sleeper agents but I have found none."

"Doc there is no way that the injuries to Mr Smith could have been caused by an untrained scientist." John said looking at him, "he is a unknown quality and I would rest easier if he was not here."

"The _Elizabeth II _should be leaving in the next few days." she pointed out, "You have released the crew and captain from isolation now."

"I know, the captain is not happy and has asked that the body be transferred to the ship when they leave." John stated "He understood my actions as commander of this city but would have preferred a joint investigation. I was going to send him on the ship before the incident anyway; I will need to send a message to the SGC to have further checks done on him before I agree to have him back in the city. I will also ask for further investigation into the crew of that ship and I want to know who that assassin was, none of the crew knew much about him, he was a technician assigned to the maintenance crews."

"Rodney told me that the data crystals that was found on his person contained schematics to the city?" she questioned

"Yes, but also star chart data, but also details on our systems and allies."

"He is a spy."

"I think so, but I do not know who for." John claimed but he wondered if it was the Alliance, "But when that ship is gone I will be happy."

He walked back to Gordon explained that it was on Dr Keller's recommendation that he was to be transferred back to Earth for further tests to find out what had caused him to lapse into a coma. Whilst his work was important to the expedition, he would need to be given a clean bill of health to return to the city.

His visit complete he began to walk up to the jumper bay, he wanted to get over to the mainland and see the progress of the construction of the two schools but he also wanted to see the progress of the three piers that were being built for sea vessels to allow transport from the mainland to Atlantis without the need for Jumpers and they could fish to get more food. The piers were also to be used as a docking point for the jumpers where they could be docked safely for immediate use.

The mainland was in John's opinion a place of great beauty that could only be rivaled by Atlantis. At the very centre of the settlement was a monument that had been unveiled only two weeks previously. An obelisk made of pure white stone which was almost opaque onto which was carved three languages and three symbols that represented the Athosians, Travellers and people of Earth. One symbol united them, the symbol the Atlantis, the city was carved into a separate piece of stone that glowed and floated above the obelisk, and even on the brightest day it could be seen glowing in the centre of the settlement.

The schools were built just outside the confines of the settlement, like much of the settlement the architects had planned for the future and allowed plenty of room for future expansion. The two schools and the clinic were the largest structures on the mainland, They had also built a tavern which was run by Kenan who had been a beer maker on Athos aswell as a farmer, it was here that they also served all manner of foods and delicacies that were acquired through trade and Lantean Cuisine.

It was a great accomplishment that they had made here on the mainland, they were now nearly entire self-sufficient. There food supplies were enough to feed them, and what they did not grow they were able to trade for. They were still supplemented by pallets of food from Earth but they were mainly commodities and branded foods and other comforts of home.

The Atlantis funding had been cut due to the financial difficulties on Earth but Atlantis could survive on its own, and make do with basic food and rations. Medicine and treatment was free to all Lanteans, Atlantis received large stocks of medicine and supplies from Earth in exchange for plants and creatures in Pegasus that offered medicinal properties, the people of this galaxy had developed many different medicines that Earth had never seen before and they were coveted.

They provided education for also but in exchange all the people of Lantea had to do their part of the society; laboring on the farms or in construction and mining, guides for the Reconnaissance Teams, men and women for the military and security teams. Even the elderly could find a work in the nurseries, gardens or many other areas of their budding settlement.

Larrin and Teyla both enjoyed time on the mainland as both of their people were integrating well, they had been very happy when it was announced that two children were expected between the three different peoples, even though the Athosians wanted to expand into a galactic trading and some of the Travellers wanted to leave they were happy and safe.

"Sheppard, the transfer to the _Elizabeth II_ has completed, the captain is requesting permission to leave the pier." Rodney told him over the radio

"I will leave now" John said and he left the tavern where he was catching up with some of his friends and journeyed back to his 'jumper so that he could communicate with them.

"Colonel Copping, we are in the green i have been told" John broadcast to the ship that he couldn't see in the distance "I take it you would like to leave?"

"Unfortunately General we are under orders to leave as soon as we are done, and the delay with the attack on Mr Matthews has already prolonged our stay, I would not be surprised if the IOA do not call soon looking for us" the reply came

"Then permission to disembark, Atlantis wishes you a safe journey" John said looking feed he opened on the HUD and patched through footage of the ship where it sat on the pier.

"Thank you Atlantis, But I had meant to warn you, there was talk back home by the IOA to have the Tria back on Earth at some point" the Colonel said "our representative has been fighting the order, just as they did for this city to return, but we believe that we may lose especially as the Protected Planets Treaty has nearly been all but abandoned and the Alliance has taken over many of the planets."

"Thanks for the warning, any help you can give us will be appreciated but the Alliance cannot gate to Atlantis, or Pegasus, and their ships cannot cross the void, we should be safe for now as long as they have not upgraded their ships beyond what Intel we have suggests." John replied and watched as the ship fired its thrusters and ascended into the into the atmosphere. "Please take care of Mr Matthews, I would like him back in one piece, but any light that you shed on the attack would also be accepted happily."

"Understood General. Good luck with your fight with the Wraith."

John didn't take the warning lightly, he traveled back to Atlantis with haste, once landed he went straight to his office where Rodney and Radek were waiting as he had requested.

"I want an update on the Tria" he told them as he took a seat.

"Well you know the hyperdrive is next to useless, We cannot reapir it as we do not have the means or even the understanding to manufacture all of the necessary parts" Rodney said "We have began to design a new drive using Asgard technology but it will take us a while to carry out the work."

"So if someone wanted to steal it how could they do it?" he said "what can we do to prevent it happening. Hypothetically?"

"Hypothetically it could be jumped into hyperspace by another vessel; all it would need is its shields." Rodney said, "Who may take it?"

"Let's just say an organisation that has their own agenda." John stated watching for their reactions.

They both sat shocked for a moment and they knew he was talking about Radek said "well if they had access to our technology, they might be able to tow it away from Atlantis, we have the technology."

"Well" Sheppard said "I want a shield generator added to the ship to protect it from a tow-link beam, I also want you to lock out navigation and propulsion, and can it be done?"

"Well the ship needs the ATA gene" Rodney said thinking out loud, "I could add a subroutine into the command matrix that will only allow a person with the ATA gene and perhaps your genetic sequence to use the ship."

"Get it done." John ordered them, "Take whoever you need."

Radek left leaving Rodney sitting their looking worried

"Who would they send?" Rodney asked

"Caldwell wouldn't as he is stationed here permanently." John said thinking on the captains of Earths ships "Sam has command of the _George Hammond_; Brigadier General Cameron Mitchell has the _Odyssey_, both of who I know and trust. Leaving Colonel Ellis of the _Apollo_"

"Would he do it, I know he wasn't happy that Caldwell was his superior but would he do it?"

"I do not know" John admitted, "he might if ordered, but there is one more ship."

"The Sun Tzu" Rodney said "It belongs to the Chinese, we should be careful if they come too, the IOA has funding from them but I wouldn't be surprised if they ordered the acquisition."

"Well I do not plan to allow that ship out of our hands, but to keep them at bay, please make sure Radek gets the ship locked to Atlantis, but I want you to finish the control chair, that should stem their attentions, the prototype works you just need to finish it."


	9. Chapter 9

**Distress Beacon**

**Chapter Nine**

Space – Milky Way Galaxy

The _USS George Hammond_ was sitting in an asteroid belt thousands of light years away from Earth, on the bridge sat Brigadier General Samantha Carter, the commission of the vessel still pleased her after commanding the vessel since its launch. She had served under the real General Hammond and she felt it a privilege to command the ship named after him.

She volunteered to have the ship used to test a new technology being developed at Area 51, using the Asgard Transport beaming technology and integrated matter stream technology they had developed a prototype mining technology using both technologies.

The ship was beaming aboard asteroids that contained raw deposits of elements such as naquadah the beaming technology would then extract the element leaving only the asteroid behind, but they were using the matter stream technology to reorganise the atomic structure of the space rock into something usable.

The second application was what was proving difficult, it was easy to create matter using energy but transforming existing matter into energy and into something entirely was not as simple as the technicians believed it would be.

Asteroid faming was hoped to be a possible way of mining materials, even with off world mining worlds it opened further options.

"General we are receiving a subspace communication from Homeworld Command" Major Kevin Marks announced.

"On Screen" Sam ordered.

"Carter?" said a voice crackling voice.

"Yes Sir" Sam said turning to Major Marks, "strengthen the signal open visual link."

It took a moment for the signal strength to increase but when it had the wall screen lit up and they could see the gruff face of Jack O'Neill

"Carter, We have received a distress signal from _HMS Elizabeth II. _For the last two hours we have attempted to make contact with her but have received radio silence, we have even sent a team to a close planet with a communication relay and have come back empty."

Sam frowned that was odd, the _Elizabeth II_ was a mark II BC:304 like her own and if it was not being detected or responding would mean that it had possibly been destroyed, or all of its crew was dead. As far as she had known the ship was on routine resupply mission.

"Where was the ship?" She asked presuming that it had fallen out of contact near the galactic void between Pegasus and the Milky Way "is it on the outer rim near the Pegasus passage?"

"No we triangulated the distress beacons location. It originated in a region of space about a hundred light-years away from the planet Kawawn." Jack told her and his face told her everything

Kawawn was a planet on the opposite side of the Milkway to the Pegasus passage, the ship should not have been there and it was not ordered by Homeworld Command.

"I know the Kawawn system is the other side of this galaxy, But do you have any idea why it was there?" She asked even thought she knew he wouldn't but she had to be sure. "I thought its mission was a supply run to Atlantis before returning to Earth for a full diagnostic on it hyperdrive after its first long distance voyage."

"It was." Jack agreed, "They should have returned to Earth three days ago, we contacted Sheppard and he told us that the ship had left two weeks ago, but he did say that there had been an incident on the City involving a crew member of the ship. A rogue crew member tried to kill an Atlantis member of staff but was killed in mysterious circumstances by a researcher."

"The ship should not have been there and we need to know what happened to it and why it was there. Your orders are to travel to the location of the beacon and investigate."

"We will leave immediately, Sir i have to warn you that if the _Elizabeth II _was destroyed then the _Hammond _will also be in danger."

"Understood." Jack said before asking hopefully "I don't suppose you have managed to develop a cloak in your spare time?"

"Sorry sir, I haven't" Sam said smiling knowing that the General was joking; "We will be careful and contact you soon."

"Good luck Sam, keep safe." Jack said before cutting the communication.

"Set a course for Kawawn." Sam told Captain Dave Kleinman the ships navigator.

"The course is set, opening the hyperspace window now." The captain said, the ship accelerated into the rift in space and into hyperspace.

"General where is this planet?" Major Marks asked.

"I have never been there, but I know of it." Sam told him "Teal'c told me of it; It used to be a mining planet of Apophis but he abandoned it when the entire population was killed by an Ashrak. Why the captain took that ship to that region of space is beyond me, there is nothing of interest in that area but hopefully we will know soon."

It took an hour and a half for them to enter the Kawawn system, they dropped out of hyperspace on the very edge of the system so that they would have advanced warning of any threats using the ship sensors.

"General we have nothing on the sensors." Major Marks told her reading his screen attentively.

"Anything on the sensors at all? energy signatures, proximity signatures, life forms, ships anything? What about the distress beacon?"

"We are to far away for life form detection, but I am reading a pocket of energy and radiation, and a large number of foreign objects. If we want to learn more we will need to get closer." He explained looking for orders "Do you want to proceed?"

"Yes, we were ordered to investigate and we need to know what happened to that ship and how it was possibly destroyed." Sam said firmly, "there may be survivors."

The _Hammond_ pushed further into the system at sublight speeds, it was not a fast way to travel but their engines were faster than most and they made good time but no amount of time could prepare them for what they saw.

They found themselves at the sight of a large graveyard. a ship graveyard.

The first ships they saw were the remains of six Ha'tak vessels, fourteen Al'kesh and a large number of Tel'taks. All of the ships were almost unrecognisable they were burnt out and full of holes and broken, with large chunks of hull and debris were drifting in space. The hull damage was consistent with a weapon that Sam was familiar with but that was not surprising as all of the burnt of ships were circling another vessel.

_HMS Elizabeth II_ sat surrounded by the ships but it was it was a sight that brought back memories of the Battle of the super gate to those that had seen it. The ship was almost entirely destroyed, nearly all of its remaining hull was blackened and was open to the harshness of space.

"Oh my god." Sam said standing up out of her seat and walking towards the window, "Are you detecting any life signs?"

"No ma'am" Kleinman told her sadly.

"She is not salvageable" Sam said sadly looking out at the entire scene "The captain was able to destroy the entire ambush fleet, this was a hard won blow to the Alliance but it is a sad day."

"General Carter, how did the Alliance even find the ship? And for that matter why was it even here?" Major Marks asked concerned.

Sam didn't answer as she didn't know, "Target the ship, no technology is to be salvaged by the Alliance or any other race." She ordered, "I would rather have the ship back on Earth but we cannot tow it, we do not have the tractor beam technology on this ship yet."

"Forward plasma batteries have the ship targeted." Major Marks announced "Do you think we should say a few words?"

Sam nodded and opened up a broadcast to the entire ship, "Here fell the ship _HMS_ _Elizabeth II_, in her short service she dealt a mighty blow to the Lucian Alliance but tragically fell with all hands." Sam said sadly "Long will you be remembered." She turned to the Major and nodded, he activated the ships weapons and four beams of plasma hit the ship in vulnerable areas which caused secondary explosions. The ships wreckage was reduced to slag and small amounts of metal.

"I want all of the wreckage beamed aboard; this will allow the science team aboard to continue with their experiments with the beaming technology." Sam ordered "But three teams are to transport over to the Alliance ships and search for information on this incident."

"General, nearly all of the vessels are registering no life support and are venting atmosphere" Kleinman reported, "Some of the Alliance ships still have an operating tansport beaming jamming field."

"Use the ring transport system." Sam said turning her back on the sight of death, "These are former Goa'uld ships so they will have rings, I am glad that I convinced the military that the Rings were not obsolete with our access to beaming technology, they have saved us from having to EVA."

Sam left the bridge to go to her office were she could report her findings privately to Earth and HWC. She reported what had happened but she also told them that it was very possible that the Alliance had not been entirely destroyed and it was possible they could have salvaged technology from the wreck.

Stargate Command – Earth

A day later Homeworld Command had received the findings of the Hammond, and it was becoming clear that the Alliance was stepping up their war against Earth and many members of the SGC were starting to feel like the Alliance was winning.

General Landry had read over the reports and had sent fifteen SG teams off world to gain intelligence on the Alliance movements but he knew that they would not find out much, what they needed was an Alliance mole but they were not easy to plant or find.

He was just making himself a cup of coffee when there was a knock on the door, he was surprised to see an old friend standing there.

"Jack! What are you doing here?"

"Officially I am not here" Jack told him and he helped himself to a cup of coffee, "and can I not just visit?"

"Jack I think I have known you long enough to know you have a reason for being here" Landry said taking a seat.

"Yes well, I supposed your right." Jack admitted, "Just got to wait for someone."

"Who –"Landry began to say but didn't need to finish as there was a light and a blurry outline of a person appeared in his office. "General Carter"

"Glad you could make it Carter, cup of Coffee?" Jack offered.

"Sir, you know I am just a hologram" Carter said "I can't drink that."

"Well it seemed rude not to ask" Jack explained smiling, he then turned to look at Landry "for the last twenty four hours I have been hounded by the British; they think we are to blame for the loss of its ship, sending it on a fool's errand for it to be destroyed."

"Well I trust you told them we did not?" Landry said surprised.

"Of course" Jack replied "The world is in a financial depression and the British banks have fallen into a rescession which means their capital is strained, they have not had the ship for even two months and it had been destroyed mysteriously, they find it odd that only our ships seemed to be untouchable."

"Our economy has also suffered, the SGC and off world expenditure has been cut in recent months, even our R&D are suffering." Sam said "But they are not the only ones believing this to be a conspiracy, I also want to know how the Alliance knew how to Ambush the ship, and even their attempts on the _Odyssey_"

"I have spoken to Sheppard about the incursion on Atlantis and the dead insurgent that arrived on the city from the ship. The man looked to have been from Earth but we have checked there is no record of him anywhere. He also held data crystals that were full of data from the Atlantis database and he seemed to want something from the Atlantis library but was disturbed by a researcher who then killed the man mysteriously and fell into a coma. Jack I have been told more by Sheppard, it seems that the ship was not only on a supply run, it was also bringing something back with them." Landry told them seriously having spent three hours speaking to Sheppard through the gate. "They took a copy of the database, consisting of data on propulsion, shields, weapons, navigational charts, element mining and refinery, manufacturing methods but also other data."

"That was not sanctioned through my office." Jack said rising a eyebrow, "This is the first I have heard of it, I thought the database had a protocols placed on it to prevent it from having the data removed?"

"It does, but it was a copy only. That enabled them to bypass the security protocols, but Sheppard had a signed ordered from your office Jack." Landry said "He didn't dial us to check as it bore the seal of Home World Command."

"I will investigate this, That order would have had to have come from me, or crossed my desk and I have never even heard mention of it." Jack told them before looking at Sam "Did you find anything at the site of the ambush or on the ships?"

"The ship was a wreck, nearly entirely burnt out, surrounded by Alliance vessels all of which had been destroyed by the ship." she explained "I destroyed the ship to prevent it falling into Alliance hands and had teams scour the wrecks of the Alliance ships."

"What did you find?" Jack asked.

"Not much" she said honestly "We found Alliance bodies in all of the ships and found this"

There was a flash of light and a flashdrive was beamed onto the table which Landry picked up and plugged into his computer, he wondered how the beaming jamming technology placed over the entire SGC had been turned off, but he assumed it was Jacks doing as he did not seem surprised. The computer took a moment to load the file and it brought up a audio file.

"_HMS Elizabeth II, _This is Brigadier General Cameron Mitchell of the _USS Odyssey_, my ships life supports systems have malfunctioned, We require your urgent assistance, your orders are to divert to our location immediately. Authentication code SG5566/HN55/KKL. Our coordinates are 78-2-36-06:01. please get here as soon as possible."

"That is my authentication code!" Landry exclaimed, "But how does Mitchell have it?"

"He didn't," Sam stated firmly "Cam came to help with the wreckage's and it was one of his teams that discovered it. However before they had arrived they had been on the Tok'ra homeworld collecting Vala."

"They finally got bored with her" Jack said shrugging in explanation, they all knew how Vala could be.

"I have run that transmission through a voice algorithm detection program and that voice was computer generated using extracts of the real Cam Mitchells voice." Sam explained further "This was an ambush, and the Alliance led the ship there."

"The Alliance has twice targeted his ship and twice he has foiled them both times and kept that ship out of Alliance hands. They know everything about us and our ships, they have been able to predict what we will do with such a decgree of accuracy I think there are more leaks, especially as they have taken over planets that fell under our protection as part of the old treaty, the moment the IOA decides to abandon the planet." Jack explained, "The Allaince threat has grown and they are winning this battle."

"What are you suggesting General?" Landry felt he had to ask even though he knew what it meant.

"We have moles." he said in a resigned voice. "and there is defiantly more than one."

"What can we do?" Hank asked "Our last sweep obviously didn't find them all as we first thought."

"No it did not, or there are sleeper cells who can brainwash our people after we have done a sweep. We need to change tact and this is off the books and cannot be made public to any one outside this room. Vala has connections all over this galaxy, and will probably know every shady dealer who deals with the Alliance. I want her to gather information regarding this attack and find out who is giving them information." Jack explained, "Mitchell is being sent on an extended secret mission, even the president doesn't know what it is but signed off on it. Jackson said he will stay on the ship to try to control Vala but he was also continue his research into the Asgard legacy, I also want the Odyssey away from Earth as that Legacy is a target."

"You know that Vala is likely to take the initiative on this mission?" Hank pointed out "how will you explain that?"

"I won't" Jack said smirking "She is not a citizen of Earth, and if she resigns as a member of the SGC she is no longer our responsibility. Earth cannot prosecute her or pass judgement on her activities off world and therefore I do not need to write a report on what she does."

"She will agree" Sam said smiling with fondness "you know how she finds our rules sir"

"Carter speak with her." Jack said carefully "express your belief that it is time for her to move on but tell her there is a business opportunity on a planet. Where it just so happens Mitchell has been dispatched to."

"So you are telling me that SG1 will not be coming back to the SGC" Landry said and he was disappointed they were his best team. "Well I suppose it is time to let you move on. I just hope that Vala makes some headway with the Alliance, her and Mitchell both have bounties on their head.

**Milkway Galaxy - Odyssey- Orbit of P4N-225**

Vala Mal Doran had resigned from her position at the SGC a day after the secret meeting between Jack and Landry. She had packed her things and been escorted to the Gateroom where she had been allowed to pick an address of her choosing so she could leave. The IOA had said that she was not to remain of Earth as she was a risk of disclosure but they also given a gate address that she should be sent to which was ignored by Landry, he didn't know anything about the planet that they suggested.

Not that it mattered which address Vala chose as the moment she was through the gate she dialed another gate and left the planet, seven times she did this to make sure that she could not be followed or tracked by the IOA or Earth before she traveled to industrial trading world and 'acquired' through her own means a Goa'uld cargo ship.

Once she had the ship she set off immediately to rendezvous with the _Odyssey_ which had landed on a planet. The cargo ship was installed with a tracking device and other systems to allow the mission to go ahead. They also scanned Vala and her belongings for any transmitters and found six which they had immediately transported off world through the gate network to six different locations. Vala made contact with people she had known back in the days when she was a mercenary and pirate and through those connections she began to trade and steal to aquire everything she needed to gain intelligence on the Alliance.

The _Odyssey_ was officially on a mission to check on planets that fell under the Protected Planets Treaty, or more correctly those that Earth still protected since the IOA had decided that Earth would no longer honor the Treaty since it used up resources.

But the true mission was to support Vala in her infiltration of the Alliance and gathering intelligence, Vala was good, but she would occasionally need help and she had asked for Mitchell's help and they had both traveled to a planet in the cargo ship, whilst the _Odyssey_ was in orbit over the planet cloaked and watching. Vala had discovered that the Planet was used by the Alliance to trade and meet with the many factions that made up their Alliance.

They had arrived at the planet a week before Vala and Mitchell had traveled down in the cargo ship, they had entered the system using at sublight speed under cloak so that they could monitor them unseen.

Seventeen vessels were detected on the planet surface and all of them belonged to the Alliance, but with the Alliance presence they had been able to find a weak link in the Alliance chain of command and someone who might have information they needed so they had traveled down to make contact.

With Mitchell on the planet the _Odyssey_ was left in the temporarily command of Doctor Daniel Jackson, he was not a military officer but was a highly respected member of SGC, and a long standing member of SG1 who stood patiently at the observation window.

"Doctor Jackson!" said the technician monitoring sensor readings.

"Please call me Daniel, what is it?" Daniel asked looking over and breaking out of his thoughts and looking down on the planet

"We are detecting seven ships are powering up on the surface" he said looking over the data, "Miss Mal Doran's ship has not powered up."

"Can you locate both Vala and Cam's locators?" he asked alarmed.

"Both of them are aboard one of the Alliance Tel'taks" the technician said and his system beeped alerting him of something, "Our Tel'tak is now powering up."

"The tracking devices that we installed will keep track of that ship, we need to follow their signals, wait for them to enter hyperspace and then follow them" Daniel ordered

"Doctor, with all due respect, you are not in command of this ship" said a major coming onto the bridge and glaring at him "you are an archaeologist. We should beam them out now."

"For now I am in command of this ship as appointed by Cameron Mitchel, Major Franks what is the position of those ships?" Daniel said sternly ignoring the man

"They have just broken through the atmosphere" the technician said and after a moment he said "they have jumped to hyperspace, our Tel'tak is currently performing a scan."

Daniel frowned thinking "this ship is cloaked, an Ancient Cloak. Their sensors will not detect us"

The ship stayed in orbit of the planet for a number of minutes before it jumped to hyperspace leaving them alone.

"Have you detected the trajectory of the subspace transmitter?" Daniel asked

"Yes sir, but our sensors will be unable to track them whilst we are in hyperspace" Franks said "We will have to drop out to track it further."

"Jump us to the closest neighbouring system" Daniel ordered, and the order was executed immediately, and they dropped the cloak and jumped to hyperspace.

**Lucian Alliance Al'kesh**

Vala was dressed in an outfit that more befitted her time as a pirate, with Mitchell in clothes that he used when impersonating Alliance members. Both were standing in the cargo hold of the ship covered by five Alliance grunts holding assault rifles.

"Boys now is this really necessary, I told you, we have information relating to the Tau'ri" Vala said calmly "If you have to have us at gunpoint, couldn't you have at least provided some bondage?" she gave one of their guards a flirty wink but received no response.

"Your charms are wasted on my men" Said a commanding voice, "I am Commander Juridah, now what information do you have on the Tau'ri?" in his hand was a hand held pistol which looked too similar to a desert eagle for Mitchel's liking.

"I have information regarding the schematics of their ships, and the weapons capabilities" Vala said "I would be happy to tell them to you over dinner"

"We are already aware of the capabilities of their ships, they have the technology of the Asgard" Juridah said "What can you tell me about that technology"

"Oh plenty darling" Vala said smiling toothily "but what will you give me in return, you have taken my Tel'tak."

"How is it you came to know this information regarding Tau'ri technology?" Juridah enquired ignoring the question, "for you to have that information you must have had access to their ships."

"I once managed to hijack one of their ships" she said "but I have since managed to infiltrate the crew of one their other ships."

"Which ship would that be? The _Odyssey_? _George Hammond_? _Apollo_? _Daedalus_ or _Sun Tzu_? We are aware that the _Elizabeth II_ was destroyed." Juridah said with a look of annoyance "Or perhaps you are not who you claim to be, and your name is not Kali or Kirk, perhaps you are a Tau'ri."

"Darling I have offered you Intel and now you insult me!" Vala said with a fake put out tone "Any information that I could give you will now have to be given to your commander. The prestige you could have got from my Intel is now beyond you."

"What about your friend?" Juridah said pointing his gun at Mitchell who glared at the man.

"Oh you can try to kill him, but I think you will find he will sooner kill you." she said and her hands clenched the strange looking belt buckle that they both had which glowed green.

Juridah didn't waste a moment and fired a shot directly at Mitchells head, but it was met with a green shield.

"Sorry bud, personal shield" Mitchel said smirking before he punch the man in the face knocking him out, the other officers were soon taken out, their automatic weapons fire useless against their shields. "I wish I had these on other missions."

"Oh yes, these would make business deals go much smoother" Vala said appreciating the device.

"Don't get used to it, we only have these two and I do not know how O'Neill got them from Atlantis but they served us well" Mitchel said they walked towards the cockpit and opened the door and dispatched of another two Alliance personnel and the pilot. "Where are we going?"

Vala sat herself in the pilot's seat and deactivated the personal shield device and bright up the navigation data, "we are flying towards the next system, according to the data we will be meeting a large group of Alliance Ha'tak's."

"We need to tell Jackson" Mitchell said "can we send a message through subspace?"

"Not if we do not want to be caught by the Alliance" Vala said and she turned to look at him "so what's the plan?"

"We need the information from the Alliance, these shields should allow us an advantage but they are not inexhaustible," Mitchell said, "we have the Reol toxin which should allow us to convince people of who we are, but we need to be careful, our faces will be known to some of the alliance."

"Yes, yes, I got the report, some stubby little colonel with a look of an angry monkey was brainwashed and passed the Alliance sensitive information about that Ancient ship galaxies away." Vala said impatiently as she looked over at the weapons that they had taken "far be it for me to say it, but they should not have these weapons, I have never seen these weapons among the Alliance."

"No" Mitchel said picking up one of the rifles and checked the magazine, before clipping it back on and cocking it and turning off the safety, "This was made back home. You should also not forget that both of us were already known to the Alliance before Colonel Telford gave them Intel."

An alert broke Vala's look and she looked down at the navigation computer "We are dropping out of Hyperspace."

They watched as the colours of hyperspace dissipated and they flew into normal space and saw that there was a large formation of Alliance ships, twelve Ha'tak surrounded by over fifty Al'kesh vessels and another forty Tel'teks but in the centre was a space station.

"This could be a problem" Mitchel said looking at them.

"Maybe, but whoever is in command here, is high up that ladder, and they will know about the destruction of that English ship, that commander here knows of it, but I would bet that he doesn't know where information comes from." Vala said and a light lit up in front of them, "We are being hailed."

"Well answer it" he said with a shrug "but power our shields."

Vala did as asked and the screen showed a Lucian Alliance Commander who scowled at seeing them.

"Where is commander Juridah?" he demanded

"He is unconscious dear, I wore him out" Vala said "the question is why were we escorted at gun point?"

"I do not know how Juridah came to capture you, but members of the Tau'ri will be destroyed, especially members of SG1" he said "Vala Mal Doran, I am aware of four bounties on your head, and Brigadier General Cameron Mitchell you too have many enemies, did you think that I would not recognise you?"

"We were hoping" Cameron said "we will be going now"

He terminated the transmission and Vala piloted them out of the convoy, but they were soon followed by the other Tel'tak's, they were dodging weapons fire attempting to get to clear space.

"Where should we jump to?" Vala asked as the ship shook as the shields were hit "we cannot survive this bombardment for long and if the remaining ship –"

"Jump us for a minute and then drop us out, Jackson should be able to pick us up before they locate us." Cameron said and he left as the jumped into a hyperspace window and quickly took a Zat' from a soldiers side arm pouch and shot them all with it to keep them down.

"Cameron we have just dropped out, how long until Daniel finds us?" Vala asked

"As long as it takes, he should have been following us." Mitchel said closing the rear compartment door in the ship and taking the co-pilot chair "can you seal them in?"

Vala not even thinking picked up the 'Zat and fired it directly at the door control, "well they cannot go anywhere now"

"And neither can we" he growled in frustration,

"Don't worry Mitchell, Daniel will be here soon to sweep me off my feet" she said happily and she looked out of the window as if expecting the _Odyssey_ to be above them. "Ah there they are!" she exclaimed seeing a window open but her face fell when seven Al'kesh dropped out of hyperspace.

They were sitting ducks, they knew that they could not survive bombardment, she began to pilot the ship to avoid the onslaught of weapons fire, the ship rattled dangerously after they were hit four times in quick succession, Mitchell attempted to fire off a shot at the oncoming vessels but they didn't have the fire power to make a dent in the shields.

Another hyperspace window opened and they both thought it must be the _Odyssey_ but again they were disappointed as a Ha'tak dropped out.

"Get us out of here Vala, cloak us then once we are clear jump." Mitchel ordered diverting all the power he could to the shields.

"Love to Cameron, but if I cloak us we are sitting hens!" Vala exclaimed as the ship was hit by a heavy bolt and they were flung from their seats, the massive golden pyramidal ship was bearing down on them menacingly.

"Another hyperspace window is opening!" Vala exclaimed frantically but the look of fear disappeared when she saw what dropped out, it was the _Odyssey_. The moment she dropped out lances of white hot plasma directly struck the armada that was surrounding them and they cut a path through the opposing ships.

"Cam, land in the Portside F-302 bay" said Daniel over an open broadcast, and Vala landed heavily inside the bay whilst the odyssey continued to fight back and cut the ranks of the Alliance. But they were safe and once they had landed the jumped away again.

Their mission was a failure but they had prisoners, and their own Tel'tak was still broadcasting but it also had further programming that was still in operation.


	10. Chapter 10

Chapter Ten

Trouble in the deep.

The Higher planes were vast and all encompassing, it was here that the Ascended beings resided, sworn only to watch and never interfere in the affairs of the mortal races.

One such being had watched over the planet Earth for a number of millennia, some could say that the being had a vested interest in its people. Long ago the being had arrived on the planet for the first time since his race had fled a great plague, but on their arrival had discovered that the humans that had once been seeded to the planet were slaves to an alien race.

He had seen the potential of the people Earth first hand when one of their race had arrived over Atlantis the day before they returned to Earth, using technology that was forbidden by the Lantean Council.

Dr Elizabeth Weir had truly inspired many of the Lantean's she was a compassionate women but she contained a hard steel that would not bend when she had been pushed. She had refused to return to Earth, she wanted to return to her people in her own time.

She had willingly sacrificed herself so that her people could live, even though it meant the end of her own life. When the Lantean's had discovered the truth of why she had not arrived on Earth, many had petitioned to return for her, but Moros had refused the request.

Earth had been a harsh and uncivilised planet when they had arrived, using their influence the Lantean's had started to sow the seeds of civilisation across the planet. They had indirectly helped with the Goa'uld uprising, but it had been one Lantean who had agreed that they would need to help further, their genes would be needed in the future so some settled into the planet.

The Ascended being watched as the people of Earth had rediscovered the Stargate and the network of gates across the Galaxy, they had found enemies but had also made great strides with technology and battles were won.

The People of Earth had been able to topple the System Lords, Replicators and the ancient enemy of the Ancients, the Ori themselves, they had even discovered the city of Atlantis and were fighting the Wraith who had defeated the Lanteans but had also discovered the mythical ship Destiny.

"They are so young, but have come so far." Said a female voice next to the man.

"As I knew they would, I saw their potential in the mind of Dr Weir." He said, "They truly are our children."

"Yes but it will be time until they become the fifth race." She said

"The Asgard were not wrong when they named them, our children are great but their growth will continue. They are the legacy of the Ancients." He told her "You know I am right."

"The Asgard named them too early"

"I do not think they had a choice." He said tiredly "Their bodies and minds were failing them, they could not have continued for much longer. The elder races are nearly all gone."

"The Nox still linger." She pointed out

"Only as a former shadow of themselves, they are reclusive and do not care for the going on of this galaxy. The Altera have ascended, the Asgard are nearly extinct with a renegade off shoot alive in Pegasus, and do not speak to me of the Furlings." He said

"They left this Galaxy a long time ago," she agreed, "But it will take time to discover where they travelled to."

"We should do more." The man declared "I hate watching but not being able to help."

"You know that you cannot, the Others will not allow it." The women said "you know what would happen, you are possibly the most closest monitored of us all."

"Two of our brethren our locked in an eternal battle, one is bound to a planet unable to help but a few humans, another's mind has splintered and will never recover stuck in the body of a human child. Even Moros took action against the Ori and was left to die when the will to ascend left him." Janus spat, "I want to do more, our benevolence is so frustrating."

"Janus you cannot help them!" the women exclaimed "You know the risks."

"Melia I tire of this existence. Sometimes I regret choosing Ascension." He said looking at Earth sadly.

"A time may come when the Ascended take to the mortal plane again, but for now you must be patient" Melia said quietly "You are not alone in your thinking, but the collective is against us."

"It would only –"Janus began but he stopped himself and looked off to the distance "Something is happening on Atlantis."

"I sense it to, We should leave." Melia said.

They transformed into their energy based forms and began to travel to the Pegasus Galaxy and to the city they once called home.

Pegasus Galaxy – Lantea – Atlantis

The city of Atlantis was mostly peaceful; it was not often that the city population was running through its halls in terror. Four hours ago a great Earthquake had rocked the entire planet. The city and settlement had felt the tremors but the Earthquake had not caused any damage.

What had shocked them was the great tsunami that had been greeted, four consecutive waves had rocked the planet and the city shield had been raised to protect the city, and the shields on the mainland had been strained to protect the settlement.

The city itself had been swept away with the waves and its connection to the underwater drilling platform had been severed and the platform had suffered minor damage which would take weeks of repairs and its crew were currently stuck on the platform.

"Rodney you should see this" Radek said from his computer

"There are many things that I need to see at this moment" Rodney said dismissively "The crew on the drilling platform are sending me data and I need to help to get it back online. We do not have the power to spare, you know that the Wraith have been in the area recently."

"Rodney, I have detected a signal from the Underwater docking clamp."

"What about it?"

"we are detecting an error with the claim number four." Radek pointed out, "the mechanism has loosened and it cannot engage. it had shifted and fallen into the ocean floor."

"Well reset it" Rodney said waiving the concern away, "It happened a couple of weeks back, the internal mechanisms are probably out of sync."

"I tried, three times, it is broken, we should send a team down to repair it."

"No, the drilling station requires our immediate attention."

"The platform is on the way to the clamp, we could have a look at it first."

Rodney finally looked up and rolled his eyes, "Fine, you want us to take a look, we will. But I am telling you it is a waste of our time."

"Yes but if we needed to submerge the city we couldn't as without all clamps functioning the city would not be anchored to the ocean floor." Radek pointed out smiling, "You know I am right so why are you fighting me."

"Because I do not want to be down there much longer that I have to be! I almost died in that jumper that crashed."

"Yes but we found you." Radek stated but muttered to himself "Unfortunately"

An hour after this conversation a group was sent out to the ocean floor to investigate the fault before traveling on to the drilling platform; seven jumpers were dispatched by only five would stop at the clamps.

Rodney, John, Major Lorne, Larrin and Doctor Becket who was back in the city to go over new medical data from Earth, the 'Jumpers had been fitted with a mark II naquadah generator to add additional power to the shields.

"Doctor McKay how certain are you that these little things will keep back the water?" Larrin asked, she had taken the gene therapy and was now able to use the technology, but she did not enjoy piloting Jumpers.

"Yes, with the additional power the water will not be a problem." Rodney explained "We will need to extend the field to push back the water around the area."

"Your sure we will be about to walk under the shield?" Becket asked "I feel a wee bit claustrophobic under this water."

"With all five ships the shields power will be combined and lower the taxation on the emitters." Radek said over the radio, "You should be careful of the whale, it is coming around to your left."

"Don't worry about the whales they are harmless" Rodney said laughing "they are quite friendly really."

"Rodney have you got any more information on the ships that were under the city?" Lorne asked "You said they were larger than our 'Jumpers."

"No, but once we can see them the jumpers sensors should identify them, the problem is I don't know there name, and finding one ship in the database is not so easy and a quick search." He stated "Radek how much further until we reach the clamp?"

"According to the sensors you should be approaching them now" Radek said "But the whale is leaving."

"It did that when we found Rodney, they are well trained to find life signs" John commented offhandedly "Switch on all exterior lighting would rather we didn't crash into anything."

They all switched on their lights and the ocean floor could be seen a little clearer and they could see a great reef of coruscations and barnacles, according to the HUD it formed a perfect circle and was several meters high.

"What is all of this?" Larrin asked

"Underwater organisms, they are created by the creatures that live here, back at home we have some great reefs." Becket explained "although I have never seen a formation like this. It's an odd place for it to form."

"This is where Atlantis sat for all those years since the Ancients left until we arrived." Rodney said "this damage would have been caused by the city rising from the ocean."

"Rodney is there a particular formation we should take?" John asked "this shield had better work."

"It will, land where I have indicated on the map. This should maximise shield strength, all hatches should face the clamp." Rodney said, it took a minute for the jumpers to settled down, the jumpers activated the full power of their shields and drew power from the on-board generators. the shield was localised around each. "I have uploaded a program to you all, activate it on my count. three, two, one."

The five shields began to expand and meld with each other until the formed a large bubble around the jumpers and the clamp, but it also pushed back all of the water.

"Well Rodney, I think you might have outdone yourself" John said, he could clearly see the docking clamp, and it became clear that it was damaged, it had dislodged itself from the base unit that was installed to the ocean bedrock.

They left the jumpers and in walked on the ocean floor, it was wet and slippery and the floor had a number of odd looking fish flapping around gasping for breath.

"Rondey! Couldn't you have pushed the fish away with the shield?" Becket asked looking at them with horror.

"Well I am sorry I was more concerned with the millions of tons of water that could crush us to death!" Rodney snapped "You're a doctor not a vet, why do you care?"

"Rodney get over here!" John commanded "You said this wouldn't take long, so how about you get started."

"Yes, yes okay." He replied and he pulled out his tablet and brought up a diagnostic system.

"How did it get damaged?" Larrin asked "I thought that Ancestor technology was very resliliant."

"We might have damaged it when we left this planet a few years ago." Rodney said "We damaged the drilling platform to, but –"

Suddenly there was a loud noise above them and a great shadow passed over the shield.

"What is that!" Larrin exclaimed pulling out her particle magnum.

"It's a whale, its probably Sam" Rodney said looking up, "What's he doing down here?"

"Rodney, that shield will not keep a whale out will it" Becket asked

"No, if it hits the shield it will collapse immediately, it must have detected us down here." He said looking at it in wonder, "just like it knew I was stuck down here before."

"Can you fix this?" John asked firmly.

"Yes, but we will need a winch to pull it back into place." Rodney explained and he turned to look at jumper four, "Well we have the winch, so get started."

The winch was hooked up to the claim mechanism and the jumper began to pulled the large mechanism back into place, it was straining the winch but eventually it pulled away from the reef, but once it moved large sections of the reef broke off.

"Becket stop!" Rodney shouted

"What is it Rodney, did I break it?" he asked

"No, Sheppard there is something in the reef!" Rondey exclaimed

True to his word there was something under the reef, and it was made of metal and glass.

John rushed into the closest jumper and brought up the HUD and immediately saw data, and it made him raise his eyebrows, it was detecting seven metallic objects inside the reef and what shocked him more was the two life signs that was being detected.

"Atlantis this is Sheppard,"

"How can we help sir?" Chuck said "We didn't expect to hear from you."

"Get a message to the Daedalus, We are going to need their help."

They waiting for a minute before Chuck replied

"They are on their way, it will take them thirty minutes." He advised.

"Tell them that to contact me when they are over our position" John ordered. "Sheppard out."

Whilst they waited they began to excavate more of the reef to see what they were looking at, and they unearthed a Lantean ship. It was not a jumper but the technology was similar, the cockpit glass had collapsed which had allowed the microorganisms into the ship.

There were no bodies but it was not surprising as they would have been eaten, but the technology was clearly Ancient but it was severely damaged, they had been able to locate a further two of the ships but couldn't access the ones with life signs.

"How can there still be lifesigns?" Larrin asked "If they are Ancestors they would be thousands of years old."

"Back home we found an Ancient who was frozen but was able to survive in a kind of stasis, but we also found another Ancient, Moros who had been the high councillor of Atlantis before returning to Earth who had been in stasis for just as long and was alive." Becket said "But they will be weak, they can survive hundreds of years but they will suffer the effects"

"So they could be true Ancestors?" she asked in wonder, "if that is true we need to help them, they may be able to help us."

"What I want to know what type of ships are these?" John asked looking at it.

"Transport vessels" Rodney said walking out of the jumper "they are Ancient Transport vessels, used for different uses they are larger than the Jumpers and cannot go through the gates but they are more like shuttles."

"Will the Daedalus be able to lock onto the ships using transport beams?" Becket asked

"Yes, but we will need to create a signal they can lock on to." Rodney explained and he pulled his bag off his shoulder and pulled out a bunch of beacons, "we used to use these back when we didn't have the Asgard sensors but they can be used to tag the ships."

Twenty minutes later the Daedalus arrived and they were able to lock onto the ships without the beacons and they were beamed directly into the beaming buffer and taken to Atlantis.

Rodney and the engineers managed to fix the docking clamp after a further thirty minutes and they were finally able to leave the ocean floor. John decided that the ships were more important so they journeyed back to the city.

Sam had followed them for a time before he had left for another part of the ocean, which made them less nervous.

The Daedalus had beamed the ships directly onto a pier and technicians and scientists streamed onto the pier to begin work. They were able to strip back all of the coral and sea life and they were finally able to access the rear compartments of the ship with the life signs.

The rear compartment had been flooded and damaged but inside they had found four pods that were obviously Lantean in origin.

The pods had been transported directly to the infirmary to be monitored by Doctor Becket and Keller. It was hoped that they would still be alive but Rodney had told them that it was unlikely as the pods were nearly dead, and without power it was unlikely that the occupants would be in good shape.

"Colonel Sheppard, We have uncovered the pods." Becket said over the radio, "you might want to get down here."

"I am on my way."

Doctor Keller and Becket looked over the pods, the technology was Lantean, but their scans told them that the pods power supply was nearly entirely depleted.

"Carson have you found any way to open them?" Jenifer asked walking over with a hand held device developed by Earth.

"No, but I think I might have an idea." Carson replied "this here looks like an interface panel."

He placed his hand to it and the pod lit up with bright blue light, which was immediately mirrored by the second pod and Data began to stream to the monitors.

"Here we go." Carson said smiling "They are alive but barely."

"Carson!" Jenifer shouted.

Turning he saw that the pods lighting turned to red and the pods sparked before all light died on the pods.

"Life signs are no longer detected" Jenifer said using her scanner "but power is still registering?"

"I see that, but –" Carson began to say moving towards the other pod but green light sprang out of the pods and scanned the room once they detected the doctors another light beamed directly to their heads and they fell unconscious.

SGSGSGSGSGSGSGSGSGSGSG

Who was discovered down in the deep?


	11. Chapter 11

**Chapter Eleven**

**Ancient Slumber **

John walked into the infirmary expecting to find the two pods being studied by Doctor Becket and Keller but he was surprised to find that instead he found both doctors laid on beds hooked up the monitors unconscious.

"What happened?" he asked walking towards the team of medical personnel who were pottering around looking busy. "Doctor Phillips?"

"We're not sure; we found them unconscious next to the pods." He said looking up from his notes "We have only found once area of concern, take a look" he brought up an ongoing scan of the brainwaves of both doctors and it was immediately obvious that it was not usual.

"Well that cannot be normal." John commented, the activity looked unnatural.

"No its not, I cannot explain what is causing these brainwaves but the security footage was disrupted momentarily and there was an energy signature. I can only guess that these pods have done something, Doctor Beckett was attempting to open the pod when the feed was cut. Now the pod systems are dead, as are the occupants."

"Doctor Phillips! Doctor Beckett is waking up!" said another medic.

Beckets eyes opened and he looked confused.

"Comdo asordo.!" he asked trying to get up "indeo Moros ut Janus?"

"Carson?" John said moving forwards to prevent his friend from getting up.

"Panitete nim operor non intellego" Becket said looking a John confused "tu quis es"

"Carson I don't –" John began but was interrupted by the doctor

"Colonel he is speaking Lantean" Doctor Philips said shocked.

"Lantea?" Becket exclaimed nodding "Atlantus?"

John nodded "You are on Atlantis."

Doctor Phillips repeated what he had said and more and got a long reply.

"Well?" John asked

"This is Doctor Beckett but at the moment he is under the influence of the mind of a Lantean scientist named Atlas, he and his partner Melianna were in those pods." Dr Phillips told him "This was a failsafe in case the pods died."

John felt his blood freeze and memories of a previous accident involving a stasis pod downloading a consciousness into his own mind were brought back, as was the pain of loss, remembering Dr Weir.

"I am familiar with this technology" John said tightly "Why can't he speak English?"

"I – Speak, not Easy" Becket said and pointed at his head "mind is broken?"

"What do you mean?" John asked firmly "You have broken Beckets mind?"

Beckett or Atlas shook his head and said something in Lantean.

"He is not accustomed to our minds, they are less advanced than the Lanteans and the transfer was supposed to be used between the same species. But he can access Beckets memories."

"Doctor here" Atlas said pointing to his head "But not speaking he cannot."

"Now he speaks like Yoda!" John sighed.

"Speak more!" Atlas said "easier to learn."

"Who are you?" John asked "tell me how you came to rest under my city."

"I am Atlas, I was the protégé of Janus the leading scientific mind of Atlantis" he said "When the Lantean Council decided to leave this galaxy, My team and myself were off world, we received the subspace message alerting us to the plan and we left our experiment to return to Atlantis."

"Our ships were detected by the Wraith and a battle was fought, there had been twenty three of our ships when we left our project but on arrival to Lantea we numbered only seven, and the ships were damaged, I myself had received a grave injury to my legs when the inertial dampeners overloaded and I was thrown from my seat. We expected to be in time for the evacuation and would be able to get help but when we saw the city it was in darkness."

"Our ships could not pass the shield and our ships detected a large fleet of Wraith above the surface. We knew that we had missed the evacuation so we decided to enter stasis and wait. The plan had been to evacuate and then return to Atlantis once our forces had been rebuilt, when they did the city sensors would detect our ships and we could be rescued. I can tell by the memories of Doctor Becket and your faces that my people never returned."

"No your people never returned to this city, they either died, Ascended, or integrated with the humans on Earth." John explained carefully "Earth is the planet where Atlantis was built and had fled the plague that had killed your Ancestors."

"You are from our home in Avalon?" he asked shocked "I have only heard stories of Terra, How long has it been since the Lanteans left? How did you find the city?"

John was able to give Atlas the basics of Earth history and the Lantean was obviously impressed.

"Here in Pegasus there were only a handful of planets that we helped advance to high technological races. You however have been able to rise faster and independently, you may have had help from the Asgard but your race is a marvel. The second evolution of my race, and also descendants of my race, it is quite remarkable." He commented smiling happily, "Have you met any of my people?"

"We met a number of your people when we discovered the Tria, it was traveling to Earth to meet the evacuees that used is sub light engines to return to Earth."

"Capatin Helia?" Atlas said with his eyebrows raised "but at sub light speeds it would take thousands of years, but then you get complications of relativity, bold move, but it is not surprising that she chose that course of action."

"yeah and then she took back the city and sent us back to Earth" John told him.

"Foolish" Atlas replied and his eyes closed a little "I can see Doctor Beckets memories of her and what transpired on this city, the Asurans killed her because of her over confidence. A trait that was too common among my people."

"Excuse me Atlas? What should we do with Doctor Keller she was hit with the same energy as you" Dr Philips asked.

Atlas stood shakily and walked toward the unconscious doctor and pressed his hands delicately to her head and she immediately woke up.

"Atlas?" she asked in question.

"Melianna" he said nodding

"Our people are not here" he said sadly "I am sorry"

"Who are these people?" she asked in fragmented English.

"People of Terra and the children of the Lanteans." He told her smiling "How are you?"

"I am fading, my chamber was damaged, my pattern is fading even now." She said and tears fell from her eyes, and she looked at John "Colonel Sheppard, please may I see my home one last time?"

"Where would you like to go?"

"The operations room, I would look out over the city before my life truly ends." She said, "Atlas come with me?"

Atlas nodded and held her had as they walked to the operations tower, Rodney saw them holding hands and looked confused and was about to say something until Melianna spoke to him.

"I am not who you believe me to be currently Rodney McKay, I am only in the mind of Doctor Jenifer Keller, do not worry she will not come to any harm."

Rodney only nodded stupidly not having a clue what was happening.

Melianna and Atlas stood on the balcony overlooking the city and the sea of Lantea, the settlement was visible in the distance due to the city moving in the storm.

"I have dreamt of this moment for thousands of years." She said sadly, "Atlas our people failed."

"Yes, but our children will not." He declared "look at the settlement, look how they have cared for us and this city, I can access this bodies mind and can see what they have done. They are our legacy, they will continue, they are our greatest success."

Melianna smiled sadly and nodded "You are right as always, I only hope that they will learn from our mistakes"

"They will." A disembodied voice said to them.

"Janus!" Atlas muttered quietly "I should have known you would be here."

"Thank you Janus you have made this easier." She said and as she closed her eyes her body slumped and was about to hit the floor but was stopped by Atlas.

"She has passed, her mind has left Doctor Keller's." he said to Atlantis staff as they rushed forward to assist sadly and he looked away back out at the city "I myself could last longer but without my partner of my heart I cannot bare to live much longer, or would that be fair on Carson Beckett.

"Is there nothing you can do?" John asked "Ascended?"

"Unfortunately that is beyond me, If I had been in my own body then perhaps but it would be impossible to do so from the body of another. The only reason I am here currently is because of a neural upload from the chamber, and I am in truth an echo of technology."

"I wish we could help you further." John said sincerely "it would help to have an Alteran here."

"Alteran?" Atlas asked "You know of our origins?"

"We know a great deal about the Alterans, or Ancients as you are known back home. We even found your ship Destiny."

"The Destiny is still on its mission, after all these millennia?" he asked in wonder

"Well yeah, we have an expedition on the ship"

"It is an ancient story that is told to all young Lanteans, the ship that was sent out into the stars to find the answer to the oldest question in the universe, a question must be answered. A lonely ship that would endeavour to find that elusive answer." He said reminiscing, "My father would tell me the story of Destiny when it was time for me to sleep, and he always wanted to see it."

John shrugged "Can you not do anything, create a new body?"

"Not in the time that I have left." Atlas confessed "Even here I would need more time than I have, but I can give you a gift. You have used Atlantis well, but it can be so much more if you allow it to be, it had taught you much but there more.

"Like what?" John asked

"Further access to the Atlantis Database, consider it a gift from an uncle."

He walked inside and used the terminals to access the database, and sat for an hour going over pages of data before he entered a portion of the database that they had been trying to access since they found Atlantis.

"I have been reviewing your own entries into the database, and the cities analysis of you. I can see that your ships are small but they possess advanced technology that you have collected, developed and been gifted. But to just give you full access would not allow you to develop, you would just adapt our technology to your needs. No I will give you small amounts of information that will hint at further advances possible if you apply your minds to it. "He said firmly "better to walk with full knowledge, than run and fall because of a lack of insight."

"I have unlocked pages of research materials on Lantean alloys and materials used in our technology, crystal technologies, Naquadah power generation data, and also research notes on hyperdrive, shields, and propulsion technologies. Since you have discovered the Destiny I think you will find the data on the ship intresting and it will help your people, its old technology but study it closely, its technology only advanced into what you see around you today on Atlantis."

"Not to sound ungrateful but what about the ZPM's?" Rodney asked hopeful "We have to hunt of them."

"I cannot give you access to that technology, you do not understand it yet, But I did add a new gate address to the Ancient Database, it was where I was conducting an experiment, we were beginning to ready the planet for terraforming using an Exogenesis device. Recover the device and you too will be able to terraform a planet, but the process requires large amounts of raw power, and the ZPM's were used readily. Twelve of them were on the planet when we left, they should still be there when you find the planet. Be warned the planet is not fit for habitation and is toxic and irradiated."

"Sorry did you say twelve?" Rodney spluttered looking like a little boy who just got his first bike for Christmas.

"Yes, do with them what you will but I would advise you to do so sparingly, you currently do not have the technology to create the container, or recharge them." Atlas said cryptically.

"Recharge them? Is that possible? And what are the coordinates?" Rodney asked pouncing on this new information

"You will need to work it out for yourself. Now I think I have imposed to long on Doctor Beckets body, Thank you for your rescuing me and allowing me to say goodbye to Melianna." Atlas closed his eyes and his body collapsed.

"Get Beckett down to the infirmary" John said to Doctor Phillips, "Rodney I want you science teams to go other all the new database entries and we need that technology and please find the planet he was talking about."

John looked back out at the planet and saw that large clouds were forming and thunder trumpeted and rocked the air, lightning shot across the sky suddenly, it was not the first time sporadic storms had appeared over Lantea and for some reason John didn't think it would be the last.

**Higher plane - Lantea **

"Janus calm down" Melia said "you could not have helped them, we did not know they lived."

"I should have checked on them!" Janus said "I failed him."

"You did not, we did not know that his team lived, had we have known we could have tried to help him, the Others might have allowed it."

Janus shook his head, "They would not have allowed it as Atlas was my son!"

"No, we could not help him as he no longer has his own body, even if he did have his body you would not have been allowed to help him ascend; Oma was punished for it and so to would have you."

"One of these days the Others will have to realise that the rules are wrong."

"They are not wrong, we are not the Ori." Melia said "We cannot become what they are, even if it means people suffer. It is the truth and you know that."

"Well if I cannot help Atlas to ascend, there is someone who I can help." Janus said cryptically and he transformed and sped away from Lantea, he was looking for something that he knew would probably get him in trouble but today he did not care.

He found himself where he needed to be and using his power as an ascended being he changed the fabric of the mortal world, in front of him light poured out of a being, and they ascended after years of being stuck they were free.

"Hello" he said to the person in front of him

"Who are you?" they asked

"In another lifetime we met" Janus said smiling "But for now you are the first step in my plan. But my name is Janus."

"You are the scientist, it was you" they said surprised "She said you liked to break the rules."

"I do, but only when they need to be broken." He said smiling "Now we need to move before we are found."

"But why did you do this, why help me?" they asked

"Because I felt you deserved it, and the universe needs people like you." He told her "you are respected even to the other Ascended beings."

"Where do we go now?" they asked

"Now we allow you to see those that have missed you greatly" he said to the women in front of him "I has been a long time since you have truly seen them, and I think you will be surprised."

The two ascended beings left the cold vacuum of space and travelled to Atlantis where they observed the people without being seen, the other ascended beings new what Janus had done but had done nothing to punish him yet.

When the women saw who was sitting in the chair that had been hers so long ago she smiled

"John, I knew you were special when we first met, but never did I think you would take that chair." She said happily. She walked behind him and placed a comforting hand on his shoulder as he sat reading over a report, the office was not tidy and she could tell that he did not like where he was but he preserved.

"He took control of the city when the IOA decided to abandon this galaxy, and destroy the city. He stole it and brought it back where it belonged." Janus said "he has your people well, the Athosians and the Race known as Travellers are now part of Lantean Society."

"He is a remarkable man." She said "I am proud of him"

John shivered and touched his shoulder like he knew she was touching it.

"He is a good man, When he returned the city he was able to fly the city for a considerable amount of time, I never knew it was possible to stay in the chair for so long." Janus said, "If he had been born on Atlantis where we controlled it he would have been a fine ship captain."

"Where shall we go now?" She asked

"Now we have to travel a long distance to find someone I think you might have met before." Janus said cryptically, "Are you ready?"

She looked at the city, she saw all of her friends but she knew they could not see her, but she did not mind for she could finally look at them without wondering if they were her own thoughts. She was about to leave when she caught sight of herself in the reflection of the glass in front of her, and saw her own face staring at herself.

Ascended beings could see themselves in mirrors and reflective surfaces even if mortals could not, but a part of her mind wondered if this explained how some people would swear they saw something in a mirror that was not there at all.

But there was one thing the women knew for certain, She would return, and Atlantis was her home.

She turned back to John "I will see you again soon John, you can count on that."

"Come Elizabeth, there is a great deal of work to do." Janus said and he held out a hand for her to take,

"Then let us begin" Elizabeth Weir replied and she took his hand and they left the City.


	12. Chapter 12

**Chapter Twelve**

**Comets Path**

**_Milky Way Galaxy – Hilipta – Lucian Alliance farming planet_**

Whilst the battles with the Wraith occupied the Atlantis Expedition, the Battle against the Lucian Alliance still plagued the Milky Way.

The Free Jaffa Nation had managed to rebuild a capital on Dakara which rivalled the previous and the new form of government was taking shape, relations between Earth and the FJN were not at their best, Earth had once been a staunch ally, but now the IOA had decided that it was time for the FJN to stand on their own.

The IOA's decision was not fully abided by, the Hammond and Odyssey often visited Dakara their captains were friends of the Jaffa and tried to help when they could, a decision that the SGC supported unofficially. The FJN had also chosen to update their fleet, Bra'tac had made sure that the traditions of the past were stuck to but he wanted the symbol of the Goa'uld was eliminated.

There Ha'tak vessels had undergone great changes to the design, the golden pyramid that had identified them was now gone, in its place the black outer design had been kept and the space that had once been taken by the pyramid had been filled with further black outer armour. The bridge was built into the top of the ship in a full circle to allow views from all angles.

Other than appearance the ship was mostly the same, the FJN did not possess much in the way of innovation, their culture was still being changed and they adjusted to being free and self-governing.

On the other side of the Galaxy the Tok'ra were also building their own home world and fleet. Their capital was a sight to behold, during their war with the Goa'uld they had used their crystal technology to create subterranean tunnels to conceal their existence, but now free of oppression they had built a great city.

They had built a large stone pyramid on the desert planet, it was made of smooth white and black stone, its interior now contained the full written history of the founding of the Tok'ra and their efforts to free themselves and destroy the System Lords. They had many virtual images of important events also shown to give a full history.

Two entire floors was dedicated as a memorial to the Tok'ra that had fallen during their patient uprising, the pyramid whilst a symbol of the Goa'uld was kept as the Tok'ra were the same species who had a different philosophy in life but that is where similarities ended. They had created crystal towers to house their small population but the city to some from Earth resembled Atlantis.

The planet was not well known to the Galaxy as they had moved the gate from another planet; they were still a cautious people and continued to hunt from minor system lords who were still alive. They had also stopped all communication with Earth, The agreement of possible willing hosts for them to inhabit had been agreed many years ago, but now the IOA had passed a law that no government can allow its people from becoming slaves to alien races.

This meant that the Tok'ra would not be able to take a human from Earth as a host, and it was clear that the IOA found the entire affair disgusting and they had insulted the Tok'ra greatly. All communication between the two planets had stopped entirely, but reports had been written of the new ships that the Tok'ra now possessed.

Their mother ships were now much longer, they still contained a pyramid, a three sided one that was golden, the remainder of the ship was white and its overall shape was triangular. The Tok'ra technology was superior to the FJN, they used technology from the ships Anubis built, stronger shields and more powerful hyperdrives. But the Weapon systems that they employed were ion cannons that they had acquired from their fallen allies the Tollan before they had been killed.

However both the FJN and the To'kra had an alliance with each other to combat the threat of the Lucian Alliance, both knew that the Alliance was focused on Earth but their own ships would be desired to replenish the Alliance fleet. They both shared all intelligence regarding Alliance operations and worked in tandem to protect their worlds.

The Alliance had grown further in numbers and strength, since the failed ambush of Elizabeth II and the failed coup on the Odyssey, they had been able to take over many planets that fell under Earths protection and with the Asgard dead they could not enforce the old treaty. Of course it helped that Earth Governments were ignoring the treaty, but had allowed alliance to further their own agenda.

Earth was in a state turmoil as the governments could not agree on a course of action and with the financial crisis that was hampering investment into the Stargate program, the Alliance had attempted four attacks on Earth all of which had been stopped by the ships in orbit but it was becoming hard to hide the existence of life in the universe from the general populace.

President Hayes had nearly been assassinated by an Alliance infiltration cell but they had not been able to gain further information from him as he had been killed by the Secret Service.

Jack sent the Odyssey and Hammond to planet that they had received intelligence on, it was said that three four Alliance Commanders two of which were key members of the Alliance, the intelligence suggested they were the fourth and fifth in command of the entire Alliance.

The planet was a rich green planet which was a planet were they were growing Kassa, and its inhabitants were also hooked on the plant and forced to mine it by the Alliance.

The _Odyssey_ and _Hammond_ dropped out of hyperspace and were started by what they saw, five Alliance ships one of which was a former mother ship of Apophis from the design. The moment the left hyperspace the Alliance ships powered towards them as fast as they could.

"Sam do we engage? Cam asked over the radio.

"We don't have a choice." She replied "We need to strike at the Alliance but I am detecting odd power signatures from that mothership."

"Okay well let's go weapons hot." Cam said and turned to his weapons officer. "All Asgard weapons are to target that mother ship now. Rail guns target the other vessels."

"Yes sir" the officer said and immediately lances of plasma energy shot from his ship and Sam's and hit the mother ship head on.

But the ships shields did not buckle under the power of the weapons.

"Sir their shields are holding!" the officer said "Detecting only a decrease in strength."

"Sam!" Cam called over the radio

"Yeah I am as shocked as you –"she said "my sensors are also picking up a cloaked cargo ship fleeing the system."

"With the ZPM augmenting the Odyssey I should be fine, get that ship and find out who is on board." Cam asked

"Okay, this shouldn't take long" Sam responded and this ship manoeuvred away from the battle but the ship was still targeted by the Alliance.

"Sir they have released gliders!" the helmsman announced.

"Well guys and girls we will just have to hit them where it hurts." Cam said smiling "All F-302's engage the gliders. Get us close to those ships and be ready to lose missiles, rail guns open fire and plasma beams target the mother ship, that should bring its shield strength down.

The Ha'tak and Al'kesh were firing consecutive bolts of energy at the ship but the shields held but were slowly losing strength under to barrage of weapons fire, but they had managed to destroy seven Al'kesh easily.

"Shield strength on the mother ship is fluctuating sir, but I am detecting a powerful energy surge." The Helmsman announced.

"Keep all batteries firing on that ship; it should be weak enough to penetrate now." Cam stated and true to his word the mother ships shields broke under the stress of a twelfth plasma beam.

"Sir the energy is still building in the ship" the officer said

"Okay, get us out of here, emergency sub light speed!" Cam ordered "Transfer all power to sub light engines, cut power to rail guns and transfer power to the Plasma beams fire on the remaining ships in quick succession."

"Cam we have caught the cargo ship, it tried to jump to hyperspace but I locked onto it with a transport beam." Sam reported but the mothership exploded and the shockwave was powerful enough over power the shields on the Odyssey and broke their sub light engines preventing them from escaping.

The whole ship rocked from the impact and nearly every system turned off and all power was diverted to the shields. Vala sat at the controls of the shield relay station on the bridge and extended the power of the shield emitters from the front to cover the depleted rear section whilst the ZPM gave the additional power necessary to maximise the shield to over the rear.

"Cameron this will not last long!" she alerted him "This is overtaxing the front shield generators."

"Understood" Cam said "Sam, can you give us a hand?"

"We are coming up behind you now Cam" Sam said

"Sir the Hammond is directly above us and is getting closer" the officer said "What is she doing?"

"Sam?" Cam asked unsure.

Above the Odyssey the George Hammond manoeuvred so it was directly over it, they were very close and it was possible to see the crew in the windows of the ship, the Hammond extended is shields, further than Cam thought possible and wrapped them within their own shied, and a lance of blue light shot from the underbelly and hit their shield.

"Cam, I need you to extend your shield like I have." Sam instructed "Then I will jump us to hyperspace."

"Vala?" Cam asked

"Don't ask me, I am out of my depth darling" she said and was quickly replaced by an air force officer who complied and Hammonds tractor beam hit the ship and they began to move.

"Opening Hyperspace window now!" Sam said and the fabric of the universe opened and the two ships flew into it and were enveloped in the blue swirling mass of subspace.

"Cam you should know that this had probably knocked us off course" she said "The shockwave will have altered are trajectory."

"Understood, now tell me who did you find in that cargo ship?" he asked

"Matthew Riley, a scientist with the IOA" she told him.

"Now why is a member of the IOA out in these neck of the woods" Cam asked "consorting with the Alliance?"

**Milk Way – Earth**

Whilst the George Hammond and Odyssey were on its mission, the Sun Tzu had been sent to a mining planet to pick up a consignment of trinium and Naquadah from a mining world to begin construction of a new ship, whilst the Apollo was currently on a mission flying through the sols system performing a series of scans on all of the planets in the system.

They were within the dust clouds of Saturn and their sensors could not sense anything out of the planets cloud bank, they were looking for any rare materials or minerals in a hope of understanding neighbouring planets better, they would eventually try to sweep over Mars but as it was monitored by Earth closely the chances of being detected were higher.

If the Apollo had been in orbit over Earth it would have been able to warn them of three objects that appeared seemingly out of now where and plumed into Earth's Atmosphere and became great balls of fire as they travelled at great speed and caused mass panic over the countries they travelled over, luckily all by one had burnt up but one had crashed into the Earth.

**_Earth - Nevada - Allied Stargate Technology Development Division (Area 51)_**

It had been twenty hours since the three consecutive comets had flown over Earth and the SGC, Homeworld Command were still no closer to discovering why they had had no warning of these events.

General Jack O'Neill had immediately ordered a full investigation into the malfunction of Earths Long Range Sensors that had failed to detect the comets, and then had conveniently turned off when they hit the atmosphere. But the investigation did not stop there, at the same time as the sensors turned off the hundreds of satellites, radar stations and even telescopes had failed to spot the oncoming comets, it was like they appeared out of nowhere.

Jack was of the opinion that this was possibly a failed attempt to strike Earth by the Lucian Alliance, but whilst the attack failed it worried many of the senior members of Homeworld Command that their systems could be deactivated when the Alliance needed them to. The hunt for informants had come up short, they knew they did not find them all and Jack believed they were silently waiting even now to stab in in back.

As part of the investigation into the comets the ASTDD had sent a full contingent of scientists to the British Isles where the only recoded had occurred in the Scottish highlands. But once they had landed they were not able to go much further as British authorities refused to acknowledge their requests for access to the site.

Eventually the team had been able to leave the airport once strings had been pulled politically but when they arrived at the site and found that it had been cordoned off by the British Army. They had refused to allow them to enter the site and no amount of political pressure had bent the British to allow entry.

The British Prime Minister Elliot Cavendish had told the IOA, and the US, Russian and Chinese that the British Army and the MOD would investigate as the impact had happened on their soil and pointed out that they had no authority over British affairs.

In Ireland and India where the other two comets had passed over, the same response was given. No remnants of those comets had been found but they were following the British example of not being pushed around by the IOA.

They had not been uncooperative, samples had been taken from the crater and they had been given to the Science team from the ASTDD. They had then been escorted to the closest airport by a private military force in place SUV's and hastened onto a plane that was waiting for them.

The British ruled that it was just a stray comet and it was a miracle that it had not hit a residential area. Further enquiries would be ongoing but they felt that there was no further danger, the private military were from Britain's Stargate personnel and they would be containing the site.

One of the scientists who had been sent to Britain was Dr Bill Lee, a specialist in alien technology who was currently stationed at the ASTDD to develop a new standard weapon for SG teams and the fleet personnel. During the course of the program they had encountered the Goa'uld Zat'nik'tel and Ma'Tok staffs, Ori staff weapons and stun weapons, the Traveller Particle Magnum, Asuran pistol, Plasma pistol and even the Wraith energy weapons.

All Earth had been able to develop was the X-699 and it was a crude and bulky weapon that would not be used in standard combat. Bill was attempting to find a way of replicating the technology for mass production but so far he had not made any headway.

His tests on the samples of space rock and residue had confirmed that the rock was indeed a standard piece of space debris, and it matched other known debris that had fallen to Earth in the past but the samples would not give any further information so Dr Lee chose to look on the internet for more information but found only UFO fanatics who were posting about the rare event.

But what Dr Lee found strange was that there were no images or videos anywhere of the comets entry into the atmosphere, he checked social networking sites and video sharing sites but found no results. Online chatter had been loud and some were blogging about how there was no visual evidence of the event and wondered if it was being covered up.

The comet had plummeted to the Earth very fast and Lee thought it unlikely that there would be footage of its entry but he wondered why nobody had thought to take a picture, but he did not think that anything was being covered up, since there was no proof of a space ship re-entry.

One online blogger had posted an article that caught his attention.

**_Fireball crashes in Scotland, government says that it was a comet, but it looked like a UFO!_**

**_I saw the fireball plummet to Earth, and I swear that it was not a piece of space rock, its form was too rounded and smooth to be natural, before I could even think to get a picture of the space craft it had crashed up the road._**

**_When I managed to get up to the site it had already be blocked by a private military force dressed all in black. I tried to get closer but they threatened to have me shot or imprisoned._**

**_The UK Government is covering up alien occurrences; this is another in a long string of sightings they have covered up, alone with the alien entity that lives in Loch Ness! We must protest the freedom of information is our right!_**

Under the small blog post was a link to further information of the UK's private military and another odd occurrence a month previous at the same site.

"Ah this is interesting" Bill said happily, hoping to get a look at the comets. He pressed the link but the page failed to load, and was not found. He attempted to go back to the original page and found that it had changed slightly with all mentions of private military removed.

Warning bells sounded inside his mind, he thought that someone was censoring information and whilst that was not impossible, and was often used to hide the Gate Program, he wondered why it would happen to hide references to private military.

He tried to find more information on this private military force in the UK but found no information on it, even the CIA and intelligence services did not have any information, so he focused his attention on trying to find more information on the comets and attempted to find information on the other two but found that even they seemed to only exist on blogs.

Frustrated that he couldn't find anything, he tried the Allied Intelligence Network that was used to monitor for Alliance spies and Goa'uld infiltration, it was also used to monitor the former NID members, but there was no information, which was not that odd anymore the collaboration of intelligence was no longer as good as it had once been, he tried to directly accessing the British Network Servers using his old pass key but his access had been revoked.

He did find one result on the Allied Intelligence Network and that was for an event that had happened the month before in Scotland where a military base had suffered from a communication blackout and every system had been destroyed using an EMP.

Whilst it was common knowledge that the even had happened, the files that contained the reports were not readily available and were protected by an encryption that one of the most sophisticated that he had ever seen, and his two attempts to break it only came back with a message.

==**TORCHWOOD**==

_ACCESS DENIED_

"Torchwood? Now where have I heard that name?" Bill questioned, he tried performing a search on the word but found only mentions of a TV series and its fans who believed it was real and was conducting alien research secretly in Cardiff, Wales. Finally defeated he write up a report that he would submit to Homeworld Command the next day. He locked his computer and turned the screen off and left his lab to go home.

As he opened the lab door he failed to notice his computer turn back on and bypass the password protection, but he had also failed to notice that the red webcam light had been lit since he began digging into the comet data. The computer executed a full purge of all information that Dr had found on the comets online, the websites he had visited and the message he had found that denied him information, and finally deleted his report before rebooting and displaying only the test results for the rock and turning back off.

**_Earth - United States Listening Station_**

The listening post was used to monitor all electronic signals that were used on Earth that could be accessed. Developments of technology acquired through the gate program were prohibited due to international law but mobile phones were not as advanced as some new technology used to prevent discovery.

One transmission was picked up originating from Canada and was sent across the globe and became untraceable.

_"This is Greyhound twelve, send a message to the Titan; we need to be more careful."_ A young female said with a Canadian accent.

_"Do we have a problem?"_ A second voice asked with authority.

_"No, my team will continue to keep things quiet, but we cannot silence everything, we have been noticed. Do we know what happened? "_

_"Understood, I will alert Blackhawk, it will be dealt with"_ the senior voice said and ignored the question.

_"Tell him that the new tech will be sent to him too, it will allow for faster project growth."_

_"I am aware; now get of this line it is not secured."_

The communication ended there and the American analyst wrote a report for his boss in hopes of a good lead but the information would only be filed away in favour of a lead on Alliance operatives who were situated in a powerful Utility company that operated across half the States of America.

SGSGSGSGGSGSGS

So here is the next chapter, bit of a filler sorry.

Next Chapter the will be called

The Rise of a former Empire.

And we will also see How Atlantis is getting on


	13. Chapter 13

**Chapter Thirteen**

**Power Requirements**

Pegasus Galaxy - Lantea - Atlantis 

Teyla stood looking over the great city that she called home; it has been a long five years but she had great hope for the future, Torren was nestled in the crook of her arm sleeping peacefully and she rubbed his head absently.

He was so happy here, which was very different from the small boys father, Kannan was rather restless still. He refused to live on the city and preferred to be on the mainland with many of the Athosians. Sometimes Teyla felt like he was their leader rather than she but then she considered herself a true Lantean of their society.

Of all her people she knew she had changed the most, freely giving herself to fight the Wraith with the help of the people of Earth. She wondered what would have happened if the expedition had not dialled Athos that fateful day, how many of her people would have survived, or would they have all been culled.

Torren suddenly began to cry startling her, the boy was hysterically screaming at the top of his voice.

"Torren?" she asked but her head snapped up looking to the sky "Wraith!" she hissed and she ran as fast as she could towards the control room.

When she arrived she startled them all.

"Teyla?" Amelia asked stepping from behind her station "Are you okay?"

"I sense the Wraith, Torren does too" She stated clearly "They are here."

"That's not possible" Chuck said frowning at her "We would have seen them on the sensors."

"I am telling you, I sense them." She told him glaring at him and he looked away from her unable to hold her gaze.

Amelia walked away quietly and walked into John's office where he was speaking to Mr Woolsey.

"Show me the sensor readings." Teyla asked Chuck.

"Of course." He said hastily and he brought up the data and it showed that the Lantean System was entirely clear, "It's clear, Teyla there are no Wraith."

"Teyla what's going on?" John asked her walking towards them frowning with concern.

"I sense Wraith, as does Torren." She stated "I can – "

She didn't continue as there was an urgent broadcast from the mainland.

"Colonel, I have Giali with an urgent message." Chuck said and the screen showed a Lantean security officer, recruited from the Travellers, but he was surrounded by seven Athosians.

"Giali what is it?" Sheppard asked.

"We have a number of the Athosian settlers who are claiming they know the Wraith are near." He reported, "Are you aware?"

"We have also been alerted." John told him "keep clam, we are looking into this."

"Very well, I will try to keep the settlers calm." Giali said nodding and the transmission ended.

"Are you finding anything on the city sensors?" Woolsey asked "We have never know the Athosians to be wrong,"

"No, the sensor sweeps have come back empty." Chuck explained "look." The screen showed the sensor readings again and he was right there was nothing there.

"The _Deadalus_ is out at the Alpha site, and all but three traveller ships are out in the galaxy on missions." John said rubbing his jaw "If there are Wraith I don't want to use the cargo ships."

"The _Tria_ is still docked on the city." Amelia pointed out "It doesn't have the hyperdrives but it does have sublight."

"Larrin!" John said over the radio.

"Sheppard?" she replied "What is it?"

"I need you on the _Tria_ now." He ordered "We may have Wraith in the System."

"I am on my way with a crew. Will you be joining us?" she asked and she could be heard running.

"No, But Lorne will be joining you." He said, "I want that ship in the air in three minutes."

"Understood, any idea where they are?" she asked

"No, but you are to sweep the entire system." He ordered and cut the radio signal on his ear.

"Where are Doctors McKay and Zelenka?" Woolsey asked

"They are off world; Zelenka is installing a Mark III naquadah generator to the children's planet." Teyla answered trying to sooth her crying baby.

"Rodney is with Dr Keller back on Earth." John answered "Which is where you should be Woolsey, go you have been summoned by the IOA."

"I do not think this is the time to leave." Woolsey pointed out

"No, the IOA has ordered you to return and so you shall, I do not want them coming here" Sheppard said shrugging, "And whilst you are there please ask them to release the money for a new Midway station."

"I will try but I do not think they will agree." He said and he nodded to Chuck who began the dialling sequence for Earth.

A number of minutes passed before the _Tria_ communicated to them.

"Sheppard we have done a sweep of the system and there are no contacts" Larrin reported "You are certain that Teyla's people can sense the Wraith."

"Yes," John said distractedly, and he looked at the sensor data. "What is that?" he asked pointing.

"Sir?" Chuck asked

"That there." Sheppard said pointing to a slowly moving dot.

"That is the asteroid belt." He said, "It occasionally moves."

"In this direction?" he questioned and the dot was slowly moving towards them through the belt.

"No that is not usual" Chuck responded and he focused the sensors on the belt and suddenly a signal was detected. "There is a something on a large asteroid."

"Larrin! We have detected the Wraith, sending you the coordinates." John said and he pressed the console and did as he said "Be careful, I do not know how they found us but they have been able to keep out of sight for this long, we do not want any more surprises!"

"Understood."

The moment the _Tria_ was in range of the asteroid belt they were hit by weapons fire.

"It's a cruiser that is buried in the rock" Larrin reported, "do we destroy it?"

"We don't have any choice!" John said "Activate prototype VD6655 now!"

The prototype was activated and the city detected a slight disturbance in subspace and their communications were temporally knocked out. It was a technology that they had developed in secret; it could be used to block Wraith telepathy and stop subspace messages. It was crude but effective, for advanced races they would detect the subspace burst that would scramble all messages and could track it but it could be used in this situation.

"It is done." Larrin reported ten minutes later when the communications were restored.

"Salvage what you can." John said and he turned to Chuck and Amelia, "You two speak with the science teams, I want to know how that ship entered this system without detection."

They nodded and walked off, Sheppard walked back to his office and sighed. He opened his top drawer and saw a bottle of whiskey that he kept there but he felt like someone was placing a hand on his own and he pushed it closed.

He wondered if it would always be like this, he needed company. Larrin had become a partner of a kind but she was not what he needed but a welcome distraction from his command. For the second time that day the alarm for a unscheduled off world activation sounded.

"IDC?" he asked resigned

"Yes, it is Captain Litilia of the Travellers" Chuck said and he added "One of the roaming ships."

John nodded, three Traveller ships had left Atlantis permanently, and there had been nothing that Larrin or John could do to prevent it, but it was there choice and he begrudgingly accepted it.

"Lower the shield!" John ordered and five seconds later a middle aged captain walked through the gate.

"Colonel" she said in greeting "Is Larrin here?"

"She is searching this system." He responded "I had not expected to hear from you, you made it clear you did not want help from Atlantis."

"I did not wish to form a Lantean Society." She said stiffly "But we share a common interest."

"And what is that?" he asked politely.

"The Wraith destroyed and the freedom and protection of my people – our people" she corrected herself.

John nodded and gestured for her to follow him to his office and they took a seat, and regarded her carefully, of the four captains that had left Lantea, she was his least favourite.

"Why have you come?" he asked

"I have information." She answered.

"And what is that information." He questioned raising his eyebrow.

"I want medical supplies" she bartered

"The agreement between our peoples stated clearly that information would be passed freely" John reminded her "It is in the best interest of your people to share information with us."

"It is also in my people's interest to have medical supplies." She commented

"Either you tell me what you have, or get out of this city" John snapped "You will not barter with my peoples safety and I will remind you that many of your own people call this city home!"

She regarded him carefully "You are a military man, certainly not a negotiator. But you are right."

"What is the information?"

"Our ships were scouting a planet for scrap when we detected four vessels drop out of hyperspace." She said "This planet had been culled entirely and so no ships should have been there."

"Wraith, they must have detected your ships." John said wondering why this was so important.

"That is just it Colonel, they were not Wraith." She said pointedly "my ships computers could not recognise them but one of them did, it was a species I believe that you have met in the past."

John knew who she was talking about, he knew of only two races that had access to hyperdrive technology and one of them was far superior to Earth in technology.

"Did there wear metal armour?" he asked

"Yes, they managed to severely damage one of our ships but they seemed to only want the data in our databanks." She said "We need urgent repairs."

"I will spare a repair crew, but you will not have medical supplies, we cannot spare them" he told her "We will also install the tracking devices into your ships including an emergency beacon in case your ships are in trouble." He told her "But I will warn you that our recourses are spread thin and I cannot afford to keep patching up your ships."

She nodded and stood "I should return to my ship."

"Where are your ships?" he asked

"These co-ordinates" she said pulling out a piece of paper.

"I will be back in a moment." John said and he walked into operations and had Amelia put the coordinates through the city systems to find the Lantean coordinates. He saw that they were for a star system that the AR Teams had never explored but he knew the area, he picked a planet that was unpopulated and had the coordinates changed into Traveller standard.

With these in hand he returned to the captain.

"Be at these coordinates in five days and my team of techs will be there." He said sternly "Now I believe you should leave, I have a team to prep as I have been looking for those beings for some time."

The captain left quickly and once the gate closed down he had AR-1 readied and sent to the planet where the Travellers had been ambushed for any signs of where the Vanir were hiding, he was in the middle of their brief when the gate activated from Earth.

The _Odyssey _and _George Hammond_ had gone missing and they requested that the _Daedalus_ return to Earth in case it was needed. John had declined to send the ship, stating that Earth had the _Apollo_ and the _Sun Tzu_, they only had one ship and they could go without the _Apollo_ for some time, O'Neill had told him that the ship could remain temporarily but they may call it back in a week if the ships had not returned.

What John didn't tell Stargate Command was that sixteen Hive ships were detected on the long range sensors, one of the largest groups to come near Atlantis is months and he was worried. He had no way of knowing what their intention was and he did not want to force a confrontation. They were two months away and he was hoping that they would change direction but the military in him told him they would attack the city soon.

The _Tria_ was not a fully functioning ship, even with the extensive repairs it would take months before they finished fitting the new hyperdrive, but Lantean Hyperdrives took them time to build from scratch.

Not to mention the _Tria_ did not have a ZPM to help power her, meaning she only had a limited supply of drones with the Grodin weapons not operational due to lack of sufficient power, they had discovered that the power generators built into the ship were not operating at full capacity, the Ancients had burnt them out traveling to Earth.

He left his office wearily, he wanted his bed and to block out the days stress.

"Sheppard" said a voice from behind him and he knew who it was and closed his eyes.

"Larrin, fancy meeting you here." He said in a low voice "I had thought you would still be on the _Tria_."

"She is back in the pier with your technicians bustling all over, I couldn't concentrate." She said walking closer "Besides I can think of something else to occupy my time."

Sheppard raised his eyebrow and ran his hand over the door control and his door opened to his quarters, "Well I think I can oblige" he said and Larrin smiled and slid between him and the door to enter.

"Well tonight should be interesting." He said dryly and he followed her in.

Three weeks later – Pegasus Galaxy – M912-PL7

Atlantis was abuzz with activity, Sheppard had sent out every AR team he could spare looking for the planet that Atlas had mentioned where he said there were twelve ZPM's lying in wait and he was determined to find them.

He had hoped that the address to the planet would be easy to find if Atlas had just added it but it seemed he hadn't, it was already in the Atlantis Database and that made them harder to find, but they had one clue, the planet was not habitable and was toxic.

They were using that as a basis for whittling down possible addresses, but it was slow going, especially as each planet would need to be searched thoroughly in case they were depleted of power, but they also wanted the exogenesis device.

They believed they had found the planet, and Atlas's warning had been on the mark, the atmosphere was dangerous and once they had arrived they had realised that the sand on the planet was corrosive and they teams had retreated back to the city.

The _Daedalus_ was sent in place of a team and it seemed that it was correct planet, it was devoid of life which made it easier for the ship to locate the ZPM's, they could detect their power signature once the ship entered the atmosphere.

Rodney had been gated to the planet when four Ancient bunkers were identified and the _Daedalus_ beamed him from the gate directly into the bunkers so he could find out what happened to the device.

"Doctor McKay this is Caldwell have you isolated the location of the device?" the colonel said over the radio.

McKay gave an annoyed laugh to the air and the absurdity of the colonel mental prowess.

"I have found out what happened to it yes, but I have not found where it is currently but there are two of the devices they work in pairs. But there are twelve of these stations over the planet each is linked to a single ZPM."

"Can you disconnect yours?"

"Yes but I do not want to do that yet, if I am right each bunker is built around a large underground water reservoir that is waiting for the terraforming to be completed before breaking the dam and filling this planets new oceans." Rodney stated "if I just pull the power the water will come crashing down and will trigger a mass overload in each bunker, the ZPM's are powering a shield device that is holding back the water."

"Then they must nearly be depleted after thousands of years."

"No, this planet also had high amounts of geothermic activity which the devices use, and that power is also siphoned into the shields so they will nearly all be full."

"So what do you propose?"

"Send down a team so I can show them what to do, and then once every station had somebody in place we pull them all at once" Rodney explained "I am also hoping that the Exogenesis devices will be in contact with one of the bunkers."

"Fine doctor, I will beam down a team." Caldwell confirmed.

Twenty four hours later every bunker had a team situated in the control room, the devices had been located deep within the planet crust and Rodney discovered that it utilised nanites to transform the planet from its base elements. Atlas and his team had already created the planets oceans which were sitting in the large mountains and had managed to create an atmosphere.

"I have found the devices colonel; I am sending you the coordinates now!" Rodney called over the radio and used the control panels to send the location to the ship.

"We have a lock" Caldwell confirmed "Beaming to portside F302 bay."

Rodney knew the colonel had been successful as alarms started to ring out across the bunker and the radio frequencies went haywire as all of the teams registered the same thing. A automated response to the devices lack transponder signal and the planet began the next stage of terraforming, the water shields began to power down and from the crust great swarms of nanites streamed to transform the planet surface.

"Doctor McKay we are detecting that the planet surface has ruptured and large energy surges." Caldwell reported "What is happening."

"The removal of both devices has started the next steps of the process." Rodney stated, he then patched into all channels "All teams are to pull out the ZPM's now, and be prepared for beam out."

"Doctor it will take us time to get to everyone, we cannot lock on from orbit." Caldwell warned.

"We do not have a choice, the process will drain the power to transform the planet even as it kills us" Rodney shouted "Get moving!"

Rodney scrambled to the power interface room where the loan ZPM for his bunker sat and he powered it down and the light dimmed and the module rose out of its housing, when he returned to the room he watched as all of the systems powered down.

"Caldwell! Any time!" Rodney muttered looking at his watch and he was getting anxious, the floor began to shake with the geothermal disturbances and he was all too aware of the amount of water that threatened to crash down on him if the colonel did not hurry up.

Twenty minutes later Rodney was beamed to the bridge of the _Daedalus_ where he was able to get a view of the planet

"What is happening, how many people are left." He asked looking at the chaos that was unfolding of the window.

"Three left." Caldwell said "but we are straining the shields staying in this atmosphere."

"You cannot allow the shields to falter even for a moment" Rodney nearly shouted, fear rippling in his stomach, "this around us in not just irradiated sand, they are nanites that will turn this planet into a green world, and they are capable of dismantling this ship and turning it into a forest if it wanted!"

"So what do you suggest?" Caldwell demanded "As it is we do not have the power to get to the three remaining teams."

"The ZPM's!" Rodney said clicking his fingers. "Do you still have the interface in the engine rooms?"

"They are fitted as standard on all Earth ships" Caldwell said, but Rodney didn't wait and he ran as fast as he could to the engine room where went about installing his ZPM to the ship, the ship accepted the additional power and immediately the additional power propelled the ship faster through the cloud and reinforced the shields.

They managed to beam the last two teams on board simultaneously just as the shields on the planet that held back the water failed and the bunkers were nearly flooded. The ship pulled out of the planet's atmosphere as fast as it could and they were safe.

Four Days after the Mission on M912-PL7

Sheppard had reported the mission back to the SGC on their weekly dial in, reporting that they had managed to locate twelve ZPM's that were still over half filled to capacity was a treasure trove, as was the Exogenesis device as it was a very advanced piece of technology that had been researched by the ASTD since SG1 had discovered an alien race converting a planet years previously.

The connection to the SGC had ended not one hour ago when the Gate began to dial and they received a IDC from Earth.

"Sheppard, the IOA is recalling you for a debrief" Landry told him, "They also want you to bring all of the ZPM's you recovered and send the Daedalus back to Earth."

"This was faster than I thought it would be." John said smiling "I knew the IOA would want them, but unfortunately the Daedalus is needed here."

Landry smiled back he was only following orders, ones that he did not agree with. "Then in that case I must inform you that Mr Storm will be heading to Atlantis in the next few hours, and John I should warn you that they want you out of the command chair."

"Thanks for the warning," John told him and he cut the connection, he turned to Chuck, "Please have all council members meet in the meeting room in ten minutes."

"Sir, Teyla is off-world negotiating a trade agreement with the Visirini." Chuck said quickly "She is not due back for another four hours."

John frowned he had forgotten that he had sent her on that assignment, "Kennan?"

"He is with Torren" Chuck said.

"Then ask him to attend." John said "he is the co-leader of the Athosians."

"Colonel! We have detected a subspace emergency beacon!" Amelia announced looking at a screen, "It is one of our coded bursts given to our allies if they need to contact us without the gate."

John knew that, it was a method the Rodney and Zelenka had created for worlds undergoing a culling when the Wraith blocked the gate. The device broadcast a message into subspace which the sensors on Atlantis could pick up in the background noise, to anyone else it would be impossible to understand.

"Who is it?"

"The Elarians" she said "the planet with the buried city ship."

"Dial them up now." Sheppard ordered and they immediately began to dial but the gate would not lock, "The Daedalus?"

"It is three hours away sir." Chuck said "it is running supplies to Relistanair, they would be able to pick up people for close system."

"Do it." John ordered, and he pressed his ear Piece. "Larrin, Lorne my office, now."

"On my way sir." Lorne said

"Okay." Larrin responded.

John returned to his office and began to pick up a number of things, he had no intention of remaining on Atlantis whilst the Elarians were in trouble.

"What is it Sheppard I was about to have a quick dinner before our meeting." Larrin said taking her seat when she entered just before Lorne.

"That meeting is postponed. A planet which contains the remains of a City ship is in trouble." He said "I intend to give assistance, But I need both of you to remain here and make sure the city is safe."

"Safe from whom?" Lorne asked

"The IOA, they want our ship, ZPM's and the Terraforming device back on Earth, I refused and they are sending a IOA head over to speak to me, they are going to try to remove me from command." He said "But they cannot do that if I am not on the city, I am keyed into the city as commander, so you two will be in charge whilst I am gone."

"Your IOA do not like my people Sheppard, they will not let me be in charge of your people." Larrin pointed out "they want my people removed from the city and mainland."

"Yes but so long as this city is under my command that will not happen. Now I do not know exactly who will come through that gate, it should only be one IOA man, but if they send through military personnel, stun them all and place them in the brig."

"What of my people's ships?" Larrin asked "Do you want their assistance?"

"Yes I will, but send only four." He said thinking "They should arrive an hour after I get to the planet."

"I will send the orders" she said and left the office.

"Permission to talk freely sir?" Lorne asked awkwardly

"You know I welcome it." John consented.

"You are pissing of the IOA, you are asking for trouble." He said "Do you really think it is a good idea to leave?"

John chuckled "I need to do this, I am tired of being out of the action, I was not made to sit behind a desk, but I sure won't let the IOA take control of this city. Woolsey did the job well but they will never let him back in that chair, he is one of us now."

"Do you know anything about what is happening on the planet?" Lorne asked

"No, but is what makes me so excited." John replied truthfully and he left his office quickly leaving a shocked lieutenant behind him.

Higher planes – Unnamed Galaxy – distant corner of Universe.

The Ascended being walked down the corridors of the famous ship, it reminded him of his past, and the hope of his people never had his people journeyed to the ship but a surprise had come when humans had reached it. These humans were special; they were descendants of his people, a legacy in their own right claiming a legacy of the Altera.

It had been just over two years since the crew had entered stasis, and the ship was still travelling on its mission and he checked to make sure that they would reach the next galaxy, he worried for the crew and the ship, and they were in danger of being boarded, and the ship could not protect them whilst they were in stasis.

But he noticed that within the dialling computer a lockout code had been placed, and it prevented incoming wormholes, it seemed that the young human had managed to save them all with his plan to fix his stasis pod.

The being left the ship quietly, he did not want to get into trouble, he had watched over Destiny for millennia and he did not plan to stop now.

Higher plane – Avalon Galaxy 

Within the great expanse of space which was devoid of life and planets, it was here that a battle was underway, a battle between two Ascended beings. They had been fighting for years and it was impossible for one to destroy the other without help and the Ancients would not help their fellow being in her battle with the Ascended Goa'uld.

Anubis had tricked Oma Desala into helping him ascend after he had been defeated and in retaliation the Ancients had only half descended him, she had been forced to watch her mistake cause havoc across the galaxy and kill hundreds in a war.

Inspired by the efforts of Doctor Daniel Jackson, Oma had finally confronted her mistake and hoped to find redemption in entering an eternal struggle, and the Ancients had allowed it as a further punishment for her interference with the lower planes.

Travelling through the plane as fast as they could was Janus and Dr Weir who he had recently ascended and helped escape her replicator form. Janus had shown her how to help him and they dived into the struggle and the effect was near immediate.

Anubis realised he was outmatched and with three ascended all powerful beings against one he tried to flee but Oma gathered all of her strength fuelled by the additional power of Janus and Dr weir was able not only stop him but rip him apart, and dispelled his energy with a great deal of pure force.

"You should not have done that Janus." Oma said reforming into a recognisable form.

"No, but I did." Janus said matter-of-factly "Your welcome, you have suffered enough."

"Thank you, but you with are at the mercy of the others now." She said sadly, and she turned to Elizabeth "I do not know you."

"I am Dr Elizabeth Weir, I am from Earth and formally in command of the city of Atlantis." She said with a friendly smile "I was also converted into an Asuran, but Janus rescued me."

"You are of Earth." Oma said surprised "Why I am not surprised one of your people are not breaking our rules."

"Doctor Jackson is not alone in his thinking that the Ancients should not abscond their responsibilities" Elizabeth said "I myself have wanted to meet you for many years."

"He is an unusual person, his compassion was his undoing but I cannot fault him for that" Oma said "It was he who pushed me to fight Anubis."

"He is a remarkable man" Elizabeth agreed, "Maybe in time he will return to the higher planes but somehow I do not think he will choose this path again."

"No, nor will our brethren let him" Janus said chuckling, "Come we have to move quickly, they cannot find us if we hurry."

They travelled to the distant supergate that was orbiting a blackhole which connected to the Celestis galaxy and they charged into it.

SGSGSGSGSGSG

Here is the next chapter,

Next chapter will of course be at the Tower. Hope to see you soon!


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